6BY1

E. coli pH03H9 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural evidence for product stabilization by the ribosomal mRNA helicase.

Amiri, H.Noller, H.F.

(2019) RNA 25: 364-375

  • DOI: https://doi.org/10.1261/rna.068965.118
  • Primary Citation of Related Structures:  
    6BY1

  • PubMed Abstract: 

    Protein synthesis in all organisms proceeds by stepwise translocation of the ribosome along messenger RNAs (mRNAs), during which the helicase activity of the ribosome unwinds encountered structures in the mRNA. This activity is known to occur near the mRNA tunnel entrance, which is lined by ribosomal proteins uS3, uS4, and uS5. However, the mechanism(s) of mRNA unwinding by the ribosome and the possible role of these proteins in the helicase activity are not well understood. Here, we present a crystal structure of the Escherichia coli ribosome in which single-stranded mRNA is observed beyond the tunnel entrance, interacting in an extended conformation with a positively charged patch on ribosomal protein uS3 immediately outside the entrance. This apparent binding specificity for single-stranded mRNA ahead of the tunnel entrance suggests that product stabilization may play a role in the unwinding of structured mRNA by the ribosomal helicase.


  • Organizational Affiliation

    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2F [auth CC],
JB [auth DC]
271Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P60422 (Escherichia coli (strain K12))
Explore P60422 
Go to UniProtKB:  P60422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60422
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3G [auth CD],
KB [auth DD]
209Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
Explore P60438 
Go to UniProtKB:  P60438
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60438
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4H [auth CE],
LB [auth DE]
181Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P60723 (Escherichia coli (strain K12))
Explore P60723 
Go to UniProtKB:  P60723
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60723
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5I [auth CF],
MB [auth DF]
177Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P62399 (Escherichia coli (strain K12))
Explore P62399 
Go to UniProtKB:  P62399
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62399
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6J [auth CG],
NB [auth DG]
176Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12))
Explore P0AG55 
Go to UniProtKB:  P0AG55
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG55
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9K [auth CH],
OB [auth DH]
149Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Explore P0A7R1 
Go to UniProtKB:  P0A7R1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7R1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10L [auth C5]109Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Explore P0A7J3 
Go to UniProtKB:  P0A7J3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7J3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11M [auth CI],
PB [auth DI]
72Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Explore P0A7J7 
Go to UniProtKB:  P0A7J7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7J7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13N [auth CJ],
QB [auth DJ]
142Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12))
Explore P0AA10 
Go to UniProtKB:  P0AA10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AA10
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14O [auth CK],
RB [auth DK]
122Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Explore P0ADY3 
Go to UniProtKB:  P0ADY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADY3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15P [auth CL],
SB [auth DL]
143Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P02413 (Escherichia coli (strain K12))
Explore P02413 
Go to UniProtKB:  P02413
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02413
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16Q [auth CM],
TB [auth DM]
136Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Explore P0ADY7 
Go to UniProtKB:  P0ADY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADY7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17R [auth CN],
UB [auth DN]
121Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12))
Explore P0AG44 
Go to UniProtKB:  P0AG44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG44
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18S [auth CO],
VB [auth DO]
116Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12))
Explore P0C018 
Go to UniProtKB:  P0C018
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C018
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19T [auth CP],
WB [auth DP]
114Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Explore P0A7K6 
Go to UniProtKB:  P0A7K6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7K6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20U [auth CQ],
XB [auth DQ]
117Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Explore P0A7L3 
Go to UniProtKB:  P0A7L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7L3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21V [auth CR],
YB [auth DR]
103Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12))
Explore P0AG48 
Go to UniProtKB:  P0AG48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG48
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22W [auth CS],
ZB [auth DS]
110Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
Explore P61175 
Go to UniProtKB:  P61175
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61175
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23AC [auth DT],
X [auth CT]
93Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Explore P0ADZ0 
Go to UniProtKB:  P0ADZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADZ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24BC [auth DU],
Y [auth CU]
102Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P60624 (Escherichia coli (strain K12))
Explore P60624 
Go to UniProtKB:  P60624
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60624
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25CC [auth DV],
Z [auth CV]
94Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
Explore P68919 
Go to UniProtKB:  P68919
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68919
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27AA [auth CW],
DC [auth DW]
75Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Explore P0A7L8 
Go to UniProtKB:  P0A7L8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7L8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28BA [auth CX],
EC [auth DX]
77Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Explore P0A7M2 
Go to UniProtKB:  P0A7M2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7M2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29CA [auth CY],
FC [auth DY]
63Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Explore P0A7M6 
Go to UniProtKB:  P0A7M6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7M6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30DA [auth CZ],
GC [auth DZ]
58Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
Explore P0AG51 
Go to UniProtKB:  P0AG51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG51
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31EA [auth C0],
HC [auth D0]
39Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Explore P0A7M9 
Go to UniProtKB:  P0A7M9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7M9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32FA [auth C1],
IC [auth D1]
56Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Explore P0A7N4 
Go to UniProtKB:  P0A7N4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7N4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33GA [auth C2],
JC [auth D2]
50Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Explore P0A7N9 
Go to UniProtKB:  P0A7N9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7N9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34HA [auth C3],
KC [auth D3]
46Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Explore P0A7P5 
Go to UniProtKB:  P0A7P5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7P5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35IA [auth C4],
LC [auth D4]
62Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Explore P0A7Q1 
Go to UniProtKB:  P0A7Q1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Q1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36JA [auth C6],
MC [auth D6]
38Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Explore P0A7Q6 
Go to UniProtKB:  P0A7Q6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Q6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2MA [auth AB],
PC [auth BB]
225Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Explore P0A7V0 
Go to UniProtKB:  P0A7V0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7V0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3NA [auth AC],
QC [auth BC]
206Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Explore P0A7V3 
Go to UniProtKB:  P0A7V3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7V3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4OA [auth AD],
RC [auth BD]
205Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Explore P0A7V8 
Go to UniProtKB:  P0A7V8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7V8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5PA [auth AE],
SC [auth BE]
150Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Explore P0A7W1 
Go to UniProtKB:  P0A7W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7W1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6QA [auth AF],
TC [auth BF]
100Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P02358 (Escherichia coli (strain K12))
Explore P02358 
Go to UniProtKB:  P02358
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02358
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7RA [auth AG],
UC [auth BG]
179Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P02359 (Escherichia coli (strain K12))
Explore P02359 
Go to UniProtKB:  P02359
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02359
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8SA [auth AH],
VC [auth BH]
129Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Explore P0A7W7 
Go to UniProtKB:  P0A7W7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7W7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9TA [auth AI],
WC [auth BI]
130Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Explore P0A7X3 
Go to UniProtKB:  P0A7X3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7X3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10UA [auth AJ],
XC [auth BJ]
98Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Explore P0A7R5 
Go to UniProtKB:  P0A7R5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7R5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11VA [auth AK],
YC [auth BK]
117Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Explore P0A7R9 
Go to UniProtKB:  P0A7R9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7R9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12WA [auth AL],
ZC [auth BL]
123Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Explore P0A7S3 
Go to UniProtKB:  P0A7S3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7S3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13AD [auth BM],
XA [auth AM]
114Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Explore P0A7S9 
Go to UniProtKB:  P0A7S9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7S9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14BD [auth BN],
YA [auth AN]
101Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG59 (Escherichia coli (strain K12))
Explore P0AG59 
Go to UniProtKB:  P0AG59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG59
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15CD [auth BO],
ZA [auth AO]
89Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Explore P0ADZ4 
Go to UniProtKB:  P0ADZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADZ4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16AB [auth AP],
DD [auth BP]
82Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Explore P0A7T3 
Go to UniProtKB:  P0A7T3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7T3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17BB [auth AQ],
ED [auth BQ]
80Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12))
Explore P0AG63 
Go to UniProtKB:  P0AG63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG63
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18CB [auth AR],
FD [auth BR]
55Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Explore P0A7T7 
Go to UniProtKB:  P0A7T7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7T7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19DB [auth AS],
GD [auth BS]
79Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Explore P0A7U3 
Go to UniProtKB:  P0A7U3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7U3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20EB [auth AT],
HD [auth BT]
85Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Explore P0A7U7 
Go to UniProtKB:  P0A7U7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7U7
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth AA],
FB [auth BA]
1,541Escherichia coli K-12
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
23S ribosomal RNAB [auth CA],
GB [auth DA]
2,904Escherichia coli K-12
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
5S ribosomal RNAC [auth CB],
HB [auth DB]
118Escherichia coli K-12
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains LengthOrganismImage
Valine-specific transfer RNAD [auth AV],
E [auth AY],
IB [auth BV],
LA [auth AW],
OC [auth BW]
76Escherichia coli K-12
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains LengthOrganismImage
Messenger RNAKA [auth AX],
NC [auth BX]
46Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AM [auth C6],
NU [auth D0],
OU [auth D6],
YL [auth C0]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth AA]
AF [auth AA]
AG [auth CA]
AH [auth CA]
AI [auth CA]
AE [auth AA],
AF [auth AA],
AG [auth CA],
AH [auth CA],
AI [auth CA],
AJ [auth CA],
AK [auth CA],
AL [auth CA],
AN [auth BA],
AO [auth DA],
AP [auth DA],
AQ [auth DA],
AR [auth DA],
AS [auth DA],
AT [auth DA],
AU [auth DA],
BE [auth AA],
BF [auth AA],
BG [auth CA],
BH [auth CA],
BI [auth CA],
BJ [auth CA],
BK [auth CA],
BL [auth CA],
BM [auth BA],
BN [auth BA],
BO [auth DA],
BP [auth DA],
BQ [auth DA],
BR [auth DA],
BS [auth DA],
BT [auth DA],
BU [auth DA],
CE [auth AA],
CF [auth AA],
CG [auth CA],
CH [auth CA],
CI [auth CA],
CJ [auth CA],
CK [auth CA],
CL [auth CA],
CM [auth BA],
CN [auth BA],
CO [auth DA],
CP [auth DA],
CQ [auth DA],
CR [auth DA],
CS [auth DA],
CT [auth DA],
CU [auth DA],
DE [auth AA],
DF [auth AA],
DG [auth CA],
DH [auth CA],
DI [auth CA],
DJ [auth CA],
DK [auth CA],
DL [auth CA],
DM [auth BA],
DN [auth BA],
DO [auth DA],
DP [auth DA],
DQ [auth DA],
DR [auth DA],
DS [auth DA],
DT [auth DA],
DU [auth DA],
EE [auth AA],
EF [auth AA],
EG [auth CA],
EH [auth CA],
EI [auth CA],
EJ [auth CA],
EK [auth CA],
EL [auth CA],
EM [auth BA],
EN [auth BA],
EO [auth DA],
EP [auth DA],
EQ [auth DA],
ER [auth DA],
ES [auth DA],
ET [auth DA],
EU [auth DA],
FE [auth AA],
FF [auth AA],
FG [auth CA],
FH [auth CA],
FI [auth CA],
FJ [auth CA],
FK [auth CA],
FL [auth CA],
FM [auth BA],
FN [auth BA],
FO [auth DA],
FP [auth DA],
FQ [auth DA],
FR [auth DA],
FS [auth DA],
FT [auth DA],
FU [auth DA],
GE [auth AA],
GF [auth CA],
GG [auth CA],
GH [auth CA],
GI [auth CA],
GJ [auth CA],
GK [auth CA],
GL [auth CA],
GM [auth BA],
GN [auth BA],
GO [auth DA],
GP [auth DA],
GQ [auth DA],
GR [auth DA],
GS [auth DA],
GT [auth DA],
GU [auth DA],
HE [auth AA],
HF [auth CA],
HG [auth CA],
HH [auth CA],
HI [auth CA],
HJ [auth CA],
HK [auth CA],
HL [auth CA],
HM [auth BA],
HN [auth BA],
HO [auth DA],
HP [auth DA],
HQ [auth DA],
HR [auth DA],
HS [auth DA],
HT [auth DA],
HU [auth DA],
ID [auth AA],
IE [auth AA],
IF [auth CA],
IG [auth CA],
IH [auth CA],
II [auth CA],
IJ [auth CA],
IK [auth CA],
IL [auth CA],
IM [auth BA],
IN [auth BA],
IO [auth DA],
IP [auth DA],
IQ [auth DA],
IR [auth DA],
IS [auth DA],
IT [auth DA],
IU [auth DB],
JD [auth AA],
JE [auth AA],
JF [auth CA],
JG [auth CA],
JH [auth CA],
JI [auth CA],
JJ [auth CA],
JK [auth CA],
JL [auth CA],
JM [auth BA],
JN [auth BA],
JO [auth DA],
JP [auth DA],
JQ [auth DA],
JR [auth DA],
JS [auth DA],
JT [auth DA],
JU [auth DB],
KD [auth AA],
KE [auth AA],
KF [auth CA],
KG [auth CA],
KH [auth CA],
KI [auth CA],
KJ [auth CA],
KK [auth CA],
KL [auth CA],
KM [auth BA],
KN [auth BA],
KO [auth DA],
KP [auth DA],
KQ [auth DA],
KR [auth DA],
KS [auth DA],
KT [auth DA],
KU [auth DB],
LD [auth AA],
LE [auth AA],
LF [auth CA],
LG [auth CA],
LH [auth CA],
LI [auth CA],
LJ [auth CA],
LK [auth CA],
LL [auth CA],
LM [auth BA],
LN [auth BA],
LO [auth DA],
LP [auth DA],
LQ [auth DA],
LR [auth DA],
LS [auth DA],
LT [auth DA],
LU [auth DN],
MD [auth AA],
ME [auth AA],
MF [auth CA],
MG [auth CA],
MH [auth CA],
MI [auth CA],
MJ [auth CA],
MK [auth CA],
ML [auth CA],
MM [auth BA],
MN [auth BA],
MO [auth DA],
MP [auth DA],
MQ [auth DA],
MR [auth DA],
MS [auth DA],
MT [auth DA],
MU [auth DQ],
ND [auth AA],
NE [auth AA],
NF [auth CA],
NG [auth CA],
NH [auth CA],
NI [auth CA],
NJ [auth CA],
NK [auth CA],
NL [auth CA],
NM [auth BA],
NN [auth BA],
NO [auth DA],
NP [auth DA],
NQ [auth DA],
NR [auth DA],
NS [auth DA],
NT [auth DA],
OD [auth AA],
OE [auth AA],
OF [auth CA],
OG [auth CA],
OH [auth CA],
OI [auth CA],
OJ [auth CA],
OK [auth CA],
OL [auth CA],
OM [auth BA],
ON [auth BA],
OO [auth DA],
OP [auth DA],
OQ [auth DA],
OR [auth DA],
OS [auth DA],
OT [auth DA],
PD [auth AA],
PE [auth AA],
PF [auth CA],
PG [auth CA],
PH [auth CA],
PI [auth CA],
PJ [auth CA],
PK [auth CA],
PL [auth CA],
PM [auth BA],
PN [auth BA],
PO [auth DA],
PP [auth DA],
PQ [auth DA],
PR [auth DA],
PS [auth DA],
PT [auth DA],
QD [auth AA],
QE [auth AA],
QF [auth CA],
QG [auth CA],
QH [auth CA],
QI [auth CA],
QJ [auth CA],
QK [auth CA],
QL [auth CA],
QM [auth BA],
QN [auth BA],
QO [auth DA],
QP [auth DA],
QQ [auth DA],
QR [auth DA],
QS [auth DA],
QT [auth DA],
RD [auth AA],
RE [auth AA],
RF [auth CA],
RG [auth CA],
RH [auth CA],
RI [auth CA],
RJ [auth CA],
RK [auth CA],
RL [auth CB],
RM [auth BA],
RN [auth BA],
RO [auth DA],
RP [auth DA],
RQ [auth DA],
RR [auth DA],
RS [auth DA],
RT [auth DA],
SD [auth AA],
SE [auth AA],
SF [auth CA],
SG [auth CA],
SH [auth CA],
SI [auth CA],
SJ [auth CA],
SK [auth CA],
SL [auth CB],
SM [auth BA],
SN [auth BA],
SO [auth DA],
SP [auth DA],
SQ [auth DA],
SR [auth DA],
SS [auth DA],
ST [auth DA],
TD [auth AA],
TE [auth AA],
TF [auth CA],
TG [auth CA],
TH [auth CA],
TI [auth CA],
TJ [auth CA],
TK [auth CA],
TL [auth CB],
TM [auth BA],
TN [auth BA],
TO [auth DA],
TP [auth DA],
TQ [auth DA],
TR [auth DA],
TS [auth DA],
TT [auth DA],
UD [auth AA],
UE [auth AA],
UF [auth CA],
UG [auth CA],
UH [auth CA],
UI [auth CA],
UJ [auth CA],
UK [auth CA],
UL [auth CC],
UM [auth BA],
UN [auth BA],
UO [auth DA],
UP [auth DA],
UQ [auth DA],
UR [auth DA],
US [auth DA],
UT [auth DA],
VD [auth AA],
VE [auth AA],
VF [auth CA],
VG [auth CA],
VH [auth CA],
VI [auth CA],
VJ [auth CA],
VK [auth CA],
VL [auth CN],
VM [auth BA],
VN [auth BA],
VO [auth DA],
VP [auth DA],
VQ [auth DA],
VR [auth DA],
VS [auth DA],
VT [auth DA],
WD [auth AA],
WE [auth AA],
WF [auth CA],
WG [auth CA],
WH [auth CA],
WI [auth CA],
WJ [auth CA],
WK [auth CA],
WL [auth CN],
WM [auth BA],
WN [auth BA],
WO [auth DA],
WP [auth DA],
WQ [auth DA],
WR [auth DA],
WS [auth DA],
WT [auth DA],
XD [auth AA],
XE [auth AA],
XF [auth CA],
XG [auth CA],
XH [auth CA],
XI [auth CA],
XJ [auth CA],
XK [auth CA],
XL [auth CQ],
XM [auth BA],
XN [auth BA],
XO [auth DA],
XP [auth DA],
XQ [auth DA],
XR [auth DA],
XS [auth DA],
XT [auth DA],
YD [auth AA],
YE [auth AA],
YF [auth CA],
YG [auth CA],
YH [auth CA],
YI [auth CA],
YJ [auth CA],
YK [auth CA],
YM [auth BA],
YN [auth DA],
YO [auth DA],
YP [auth DA],
YQ [auth DA],
YR [auth DA],
YS [auth DA],
YT [auth DA],
ZD [auth AA],
ZE [auth AA],
ZF [auth CA],
ZG [auth CA],
ZH [auth CA],
ZI [auth CA],
ZJ [auth CA],
ZK [auth CA],
ZL [auth C4],
ZM [auth BA],
ZN [auth DA],
ZO [auth DA],
ZP [auth DA],
ZQ [auth DA],
ZR [auth DA],
ZS [auth DA],
ZT [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.656α = 90
b = 433.909β = 90
c = 623.532γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States17129
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States59140

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2020-02-12
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description