4DR4

Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, cognate transfer RNA anticodon stem-loop and multiple copies of paromomycin molecules bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.97 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A structural basis for streptomycin-induced misreading of the genetic code.

Demirci, H.Murphy, F.Murphy, E.Gregory, S.T.Dahlberg, A.E.Jogl, G.

(2013) Nat Commun 4: 1355-1355

  • DOI: 10.1038/ncomms2346
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • During protein synthesis, the ribosome selects aminoacyl-transfer RNAs with anticodons matching the messenger RNA codon present in the A site of the small ribosomal subunit. The aminoglycoside antibiotic streptomycin disrupts decoding by binding clos ...

    During protein synthesis, the ribosome selects aminoacyl-transfer RNAs with anticodons matching the messenger RNA codon present in the A site of the small ribosomal subunit. The aminoglycoside antibiotic streptomycin disrupts decoding by binding close to the site of codon recognition. Here we use X-ray crystallography to define the impact of streptomycin on the decoding site of the Thermus thermophilus 30S ribosomal subunit in complexes with cognate or near-cognate anticodon stem-loop analogues and messenger RNA. Our crystal structures display a significant local distortion of 16S ribosomal RNA induced by streptomycin, including the crucial bases A1492 and A1493 that participate directly in codon recognition. Consistent with kinetic data, we observe that streptomycin stabilizes the near-cognate anticodon stem-loop analogue complex, while destabilizing the cognate anticodon stem-loop analogue complex. These data reveal how streptomycin disrupts the recognition of cognate anticodon stem-loop analogues and yet improves recognition of a near-cognate anticodon stem-loop analogue.


    Organizational Affiliation

    Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
C
239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
135Thermus thermophilus HB8Mutation(s): 0 
Find proteins for F6DEQ7 (Thermus thermophilus (strain SG0.5JP17-16))
Go to UniProtKB:  F6DEQ7

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
M
126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
N
61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY6

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Q
105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY7

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
J
105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
K
129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
O
89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
P
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
R
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S
93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
T
106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein THX
U
27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
D
209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
E
162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
F
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
G
156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
H
138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
I
128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAA1522Thermus thermophilus HB8
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 22
MoleculeChainsLengthOrganism
5'-R(*UP*UP*U)-3'V3Thermus thermophilus HB8
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 23
MoleculeChainsLengthOrganism
5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3'W15Thermus thermophilus HB8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download CCD File 
A
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
D, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, D, E, H, L, N, O, P, Q, S, T, V
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
L
L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.97 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 400.951α = 90
b = 400.951β = 90
c = 176.675γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references
  • Version 1.2: 2013-01-30
    Changes: Database references