4V87

Crystal structure analysis of ribosomal decoding.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A new understanding of the decoding principle on the ribosome.

Demeshkina, N.Jenner, L.Westhof, E.Yusupov, M.Yusupova, G.

(2012) Nature 484: 256-259

  • DOI: https://doi.org/10.1038/nature10913
  • Primary Citation of Related Structures:  
    4V87, 4V8B, 4V8C, 4V8D, 4V8E, 4V8F

  • PubMed Abstract: 

    During protein synthesis, the ribosome accurately selects transfer RNAs (tRNAs) in accordance with the messenger RNA (mRNA) triplet in the decoding centre. tRNA selection is initiated by elongation factor Tu, which delivers tRNA to the aminoacyl tRNA-binding site (A site) and hydrolyses GTP upon establishing codon-anticodon interactions in the decoding centre. At the following proofreading step the ribosome re-examines the tRNA and rejects it if it does not match the A codon. It was suggested that universally conserved G530, A1492 and A1493 of 16S ribosomal RNA, critical for tRNA binding in the A site, actively monitor cognate tRNA, and that recognition of the correct codon-anticodon duplex induces an overall ribosome conformational change (domain closure). Here we propose an integrated mechanism for decoding based on six X-ray structures of the 70S ribosome determined at 3.1-3.4 Å resolution, modelling cognate or near-cognate states of the decoding centre at the proofreading step. We show that the 30S subunit undergoes an identical domain closure upon binding of either cognate or near-cognate tRNA. This conformational change of the 30S subunit forms a decoding centre that constrains the mRNA in such a way that the first two nucleotides of the A codon are limited to form Watson-Crick base pairs. When U·G and G·U mismatches, generally considered to form wobble base pairs, are at the first or second codon-anticodon position, the decoding centre forces this pair to adopt the geometry close to that of a canonical C·G pair. This by itself, or with distortions in the codon-anticodon mini-helix and the anticodon loop, causes the near-cognate tRNA to dissociate from the ribosome.


  • Organizational Affiliation

    Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth AD],
EC [auth DD]
272Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth AE],
FC [auth DE]
205Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth AF],
GC [auth DF]
208Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth AG],
HC [auth DG]
181Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth AH],
IC [auth DH]
170Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9H [auth AK],
JC [auth DK]
146Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13I [auth AM],
KC [auth DM]
138Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14J [auth AN],
LC [auth DN]
122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15K [auth AO],
MC [auth DO]
150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16L [auth AP],
NC [auth DP]
141Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17M [auth A0],
OC [auth D0]
118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18N [auth AQ],
PC [auth DQ]
111Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19O [auth AR],
QC [auth DR]
137Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20P [auth A1],
RC [auth D1]
117Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21Q [auth A2],
SC [auth D2]
101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22R [auth AS],
TC [auth DS]
113Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23S [auth AT],
UC [auth DT]
92Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24T [auth AU],
VC [auth DU]
102Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25U [auth AV],
WC [auth DV]
179Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth A3],
XC [auth D3]
77Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28W [auth AZ],
YC [auth DZ]
97Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth AW],
ZC [auth DW]
69Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AD [auth DX],
Y [auth AX]
59Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31BD [auth D4],
Z [auth A4]
66Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth A5],
CD [auth D5]
59Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33BA [auth A6],
DD [auth D6]
45Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth A7],
ED [auth D7]
49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35DA [auth A8],
FD [auth D8]
61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2EB [auth CE],
FA [auth BE]
256Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3FB [auth CF],
GA [auth BF]
239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4GB [auth CG],
HA [auth BG]
208Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5HB [auth CH],
IA [auth BH]
162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6IB [auth CI],
JA [auth BI]
101Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7JB [auth CJ],
KA [auth BJ]
156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8KB [auth CK],
LA [auth BK]
138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9LB [auth CL],
MA [auth BL]
128Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10MB [auth CM],
NA [auth BM]
105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11NB [auth CN],
OA [auth BN]
129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12OB [auth CO],
PA [auth BO]
132Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13PB [auth CP],
QA [auth BP]
126Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14QB [auth CQ],
RA [auth BQ]
61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15RB [auth CR],
SA [auth BR]
89Thermus thermophilus HB8Mutation(s): 0 
UniProt
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UniProt GroupQ5SJ76
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16SB [auth CS],
TA [auth BS]
88Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17TB [auth CT],
UA [auth BT]
105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18UB [auth CU],
VA [auth BU]
88Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19VB [auth CV],
WA [auth BV]
93Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20WB [auth CW],
XA [auth BW]
106Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXXB [auth CX],
YA [auth BX]
27Escherichia coli str. K-12 substr. MDS42Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (2909-MER)A [auth AA],
CC [auth DA]
2,912Thermus thermophilus HB8
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAB [auth AB],
DC [auth DB]
122Thermus thermophilus HB8
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Entity ID: 31
MoleculeChains LengthOrganismImage
16S ribosomal RNADB [auth CA],
EA [auth BA]
1,506Thermus thermophilus HB8
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Entity ID: 52
MoleculeChains LengthOrganismImage
TRNA-LEUYB [auth CB],
ZA [auth BB]
87synthetic construct
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Entity ID: 53
MoleculeChains LengthOrganismImage
TRNA-FMETAB [auth BC],
AC [auth CD],
BB [auth BD],
ZB [auth CC]
77Escherichia coli str. K-12 substr. MDS42
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Entity ID: 54
MoleculeChains LengthOrganismImage
MRNABC [auth C1],
CB [auth B1]
10synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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JMA [auth BG],
NVA [auth CG],
OMA [auth BQ],
PVA [auth CQ]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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