4V5P

The crystal structure of EF-Tu and A9C-tRNA-Trp bound to a near- cognate codon on the 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

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This is version 2.2 of the entry. See complete history


Literature

How Mutations in tRNA Distant from the Anticodon Affect the Fidelity of Decoding.

Schmeing, T.M.Voorhees, R.M.Kelley, A.C.Ramakrishnan, V.

(2011) Nat Struct Mol Biol 18: 432

  • DOI: https://doi.org/10.1038/nsmb.2003
  • Primary Citation of Related Structures:  
    4V5P, 4V5Q, 4V5R, 4V5S

  • PubMed Abstract: 

    The ribosome converts genetic information into protein by selecting aminoacyl tRNAs whose anticodons base-pair to an mRNA codon. Mutations in the tRNA body can perturb this process and affect fidelity. The Hirsh suppressor is a well-studied tRNA(Trp) harboring a G24A mutation that allows readthrough of UGA stop codons. Here we present crystal structures of the 70S ribosome complexed with EF-Tu and aminoacyl tRNA (native tRNA(Trp), G24A tRNA(Trp) or the miscoding A9C tRNA(Trp)) bound to cognate UGG or near-cognate UGA codons, determined at 3.2-Å resolution. The A9C and G24A mutations lead to miscoding by facilitating the distortion of tRNA required for decoding. A9C accomplishes this by increasing tRNA flexibility, whereas G24A allows the formation of an additional hydrogen bond that stabilizes the distortion. Our results also suggest that each native tRNA will adopt a unique conformation when delivered to the ribosome that allows accurate decoding.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK. martin.schmeing@mcgill.ca


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B [auth AB],
IB [auth CB]
256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3C [auth AC],
JB [auth CC]
239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D [auth AD],
KB [auth CD]
209Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E [auth AE],
LB [auth CE]
162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6F [auth AF],
MB [auth CF]
101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G [auth AG],
NB [auth CG]
156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8H [auth AH],
OB [auth CH]
138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9I [auth AI],
PB [auth CI]
128Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10J [auth AJ],
QB [auth CJ]
105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11K [auth AK],
RB [auth CK]
129Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12L [auth AL],
SB [auth CL]
135Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13M [auth AM],
TB [auth CM]
126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14N [auth AN],
UB [auth CN]
61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15O [auth AO],
VB [auth CO]
89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16P [auth AP],
WB [auth CP]
88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17Q [auth AQ],
XB [auth CQ]
105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18R [auth AR],
YB [auth CR]
88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19S [auth AS],
ZB [auth CS]
93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20AC [auth CT],
T [auth AT]
106Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXBC [auth CU],
U [auth AU]
27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ELONGATION FACTOR TUGC [auth CZ],
Z [auth AZ]
405Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27AA [auth B0],
HC [auth D0]
85Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28BA [auth B1],
IC [auth D1]
98Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29CA [auth B2],
JC [auth D2]
72Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30DA [auth B3],
KC [auth D3]
60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31EA [auth B4],
LC [auth D4]
71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32FA [auth B5],
MC [auth D5]
60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33GA [auth B6],
NC [auth D6]
54Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34HA [auth B7],
OC [auth D7]
49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35IA [auth B8],
PC [auth D8]
65Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L36JA [auth B9],
QC [auth D9]
37Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L1MA [auth BC],
TC [auth DC]
229Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2NA [auth BD],
UC [auth DD]
276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3OA [auth BE],
VC [auth DE]
206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4PA [auth BF],
WC [auth DF]
210Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5QA [auth BG],
XC [auth DG]
182Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6RA [auth BH],
YC [auth DH]
180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10SA [auth BJ],
ZC [auth DJ]
173Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11AD [auth DK],
TA [auth BK]
147Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13BD [auth DN],
UA [auth BN]
140Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14CD [auth DO],
VA [auth BO]
122Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15DD [auth DP],
WA [auth BP]
150Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L16ED [auth DQ],
XA [auth BQ]
141Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L17FD [auth DR],
YA [auth BR]
118Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18GD [auth DS],
ZA [auth BS]
112Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19AB [auth BT],
HD [auth DT]
146Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L20BB [auth BU],
ID [auth DU]
118Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21CB [auth BV],
JD [auth DV]
101Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22DB [auth BW],
KD [auth DW]
113Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23EB [auth BX],
LD [auth DX]
96Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24FB [auth BY],
MD [auth DY]
110Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25GB [auth BZ],
ND [auth DZ]
206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RRNAA [auth AA],
HB [auth CA]
1,522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
E-SITE TRNA PHE OR P-SITE TRNA PHECC [auth CV],
DC [auth CW],
V [auth AV],
W [auth AW]
76Escherichia coli K-12
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Entity ID: 23
MoleculeChains LengthOrganismImage
MRNAEC [auth CX],
X [auth AX]
27Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
A-SITE TRNA A9C TRP-TRNA TRPFC [auth CY],
Y [auth AY]
77Escherichia coli K-12
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Entity ID: 36
MoleculeChains LengthOrganismImage
23S RIBOSOMAL RNAKA [auth BA],
RC [auth DA]
2,915Thermus thermophilus HB8
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Entity ID: 37
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNALA [auth BB],
SC [auth DB]
122Thermus thermophilus HB8
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KIR
Query on KIR

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RD [auth AZ],
XD [auth CZ]
KIRROMYCIN
C43 H60 N2 O12
HMSYAPGFKGSXAJ-PAHGNTJYSA-N
GDP
Query on GDP

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QD [auth AZ],
WD [auth CZ]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN
Query on ZN

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OD [auth AD]
PD [auth AN]
SD [auth B4]
TD [auth B9]
UD [auth CD]
OD [auth AD],
PD [auth AN],
SD [auth B4],
TD [auth B9],
UD [auth CD],
VD [auth CN],
YD [auth D4],
ZD [auth D9]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 289.9α = 90
b = 268.5β = 91.62
c = 403.6γ = 90
Software Package:
Software NamePurpose
CNSmodel building
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2018-11-21
    Changes: Advisory, Data collection
  • Version 2.0: 2019-06-26
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description