4V6K

Structural insights into cognate vs. near-cognate discrimination during decoding.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 3.0 of the entry. See complete history

Literature

Structural insights into cognate versus near-cognate discrimination during decoding.

Agirrezabala, X.Schreiner, E.Trabuco, L.G.Lei, J.Ortiz-Meoz, R.F.Schulten, K.Green, R.Frank, J.

(2011) Embo J. 30: 1497-1507

  • DOI: 10.1038/emboj.2011.58
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) containing the near-cognate Trp-tRNA(Trp) in the presence of kirromycin. Go ...

    The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) containing the near-cognate Trp-tRNA(Trp) in the presence of kirromycin. Going through more than 350 000 images and employing image classification procedures, we find ∼8% in which the TC is bound to the ribosome. The reconstructed 3D map provides a means to characterize the arrangement of the near-cognate aa-tRNA with respect to elongation factor Tu (EF-Tu) and the ribosome, as well as the domain movements of the ribosome. One of the interesting findings is that near-cognate tRNA's acceptor stem region is flexible and CCA end becomes disordered. The data bring direct structural insights into the induced-fit mechanism of decoding by the ribosome, as the analysis of the interactions between small and large ribosomal subunit, aa-tRNA and EF-Tu and comparison with the cognate case (UGG codon) offers clues on how the conformational signals conveyed to the GTPase differ in the two cases.


    Organizational Affiliation

    Structural Biology Unit, CIC-bioGUNE, Derio, Basque Country, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
AC
234Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplA
Find proteins for P0A7L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
AD
273Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
AE
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
AF
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
AG
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
AH
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
AI
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
AJ
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
AK
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
AL
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
AM
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
AN
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
AO
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
AP
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
AQ
115Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
AR
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
AS
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
AT
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
AU
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
AV
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
AW
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
AX
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
AY
78Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
AZ
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Aa
59Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
Ab
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmE
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
Ac
57Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
Ad
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
Ae
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
Af
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
Ag
38N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Tu 2
BC
393Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: tufB
Find proteins for P0CE48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0CE48
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
BF
241Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
BG
233Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
BH
206Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
BI
167Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
BJ
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
BK
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
BL
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
BM
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
BN
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
BO
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
BP
124Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
BQ
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
BR
101Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
BS
89Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q8X9M2 (Escherichia coli O157:H7)
Go to UniProtKB:  Q8X9M2
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
BT
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
BU
84Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
BV
75Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
BW
92Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
BX
87Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
BY
71Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 1
MoleculeChainsLengthOrganism
ribosomal RNA 5SAA120Escherichia coli K-12
Entity ID: 2
MoleculeChainsLengthOrganism
ribosomal RNA 23SAB2904Escherichia coli K-12
Entity ID: 34
MoleculeChainsLengthOrganism
16S ribosomal RNABA1542Escherichia coli DH1
Entity ID: 35
MoleculeChainsLengthOrganism
A/T-site tRNA PheBB,BE76Escherichia coli DH1
Entity ID: 37
MoleculeChainsLengthOrganism
mRNABD24Escherichia coli
Small Molecules
Modified Residues  20 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
AB, BA, BB, BE
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
AB, BA
RNA LINKINGC10 H16 N3 O8 PC
6MZ
Query on 6MZ
AB
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
AB
RNA LINKINGC10 H15 N2 O9 PU
1MG
Query on 1MG
AB
RNA LINKINGC11 H16 N5 O8 PG
3AU
Query on 3AU
BB, BE
RNA linkingC13 H20 N3 O11 PU
OMC
Query on OMC
AB
RNA LINKINGC10 H16 N3 O8 PC
MA6
Query on MA6
BA
RNA LINKINGC12 H18 N5 O7 PA
4SU
Query on 4SU
BB, BE
RNA LINKINGC9 H13 N2 O8 P SU
CH
Query on CH
AB
RNA LINKINGC9 H15 N3 O8 PC
MIA
Query on MIA
BB, BE
RNA LINKINGC16 H24 N5 O7 P SA
2MG
Query on 2MG
AB, BA
RNA LINKINGC11 H16 N5 O8 PG
UR3
Query on UR3
BA
RNA LINKINGC10 H15 N2 O9 PU
OMG
Query on OMG
AB
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
AB, BA, BB, BE
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
AB, BB, BE
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
AB
RNA LINKINGC11 H16 N5 O7 PA
4OC
Query on 4OC
BA
RNA LINKINGC11 H18 N3 O8 PC
3TD
Query on 3TD
AB
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
AB, BB, BE
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2015-03-25
    Type: Other
  • Version 2.0: 2018-07-18
    Type: Data collection, Database references, Polymer sequence
  • Version 3.0: 2019-07-03
    Type: Data collection, Derived calculations, Non-polymer description, Structure summary