RCSB PDB - 4V6F: Elongation complex of the 70S ribosome with three tRNAs and mRNA.

 4V6F

Elongation complex of the 70S ribosome with three tRNAs and mRNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.215 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6QNR


Literature

Structural aspects of messenger RNA reading frame maintenance by the ribosome.

Jenner, L.B.Demeshkina, N.Yusupova, G.Yusupov, M.

(2010) Nat Struct Mol Biol 17: 555-560

  • DOI: https://doi.org/10.1038/nsmb.1790
  • Primary Citation of Related Structures:  
    4V6F, 4V6G

  • PubMed Abstract: 

    One key question in protein biosynthesis is how the ribosome couples mRNA and tRNA movements to prevent disruption of weak codon-anticodon interactions and loss of the translational reading frame during translocation. Here we report the complete path of mRNA on the 70S ribosome at the atomic level (3.1-A resolution), and we show that one of the conformational rearrangements that occurs upon transition from initiation to elongation is a narrowing of the downstream mRNA tunnel. This rearrangement triggers formation of a network of interactions between the mRNA downstream of the A-site codon and the elongating ribosome. Our data elucidate the mechanism by which hypermodified nucleoside 2-methylthio-N6 isopentenyl adenosine at position 37 (ms(2)i(6)A37) in tRNA(Phe)(GAA) stabilizes mRNA-tRNA interactions in all three tRNA binding sites. Another network of contacts is formed between this tRNA modification and ribosomal elements surrounding the mRNA E/P kink, resulting in the anchoring of P-site tRNA. These data allow rationalization of how modification deficiencies of ms(2)i(6)A37 in tRNAs may lead to shifts of the translational reading frame.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2C [auth AD],
EC [auth DD]
276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3D [auth AE],
FC [auth DE]
206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4E [auth AF],
GC [auth DF]
210Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5F [auth AG],
HC [auth DG]
182Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6G [auth AH],
IC [auth DH]
180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L9H [auth AK],
KC [auth DK]
148Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13I [auth AM],
OC [auth DM]
140Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14J [auth AN],
PC [auth DN]
122Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15K [auth AO],
QC [auth DO]
150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L16L [auth AP],
RC [auth DP]
141Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L17M [auth A0],
SC [auth D0]
118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18N [auth AQ],
TC [auth DQ]
112Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19O [auth AR],
UC [auth DR]
146Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L20P [auth A1],
VC [auth D1]
118Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21Q [auth A2],
WC [auth D2]
101Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22R [auth AS],
XC [auth DS]
113Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23S [auth AT],
YC [auth DT]
96Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24T [auth AU],
ZC [auth DU]
110Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25AD [auth DV],
U [auth AV]
206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27BD [auth D3],
V [auth A3]
85Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28CD [auth DZ],
W [auth AZ]
98Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29DD [auth DW],
X [auth AW]
72Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30ED [auth DX],
Y [auth AX]
60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31FD [auth D4],
Z [auth A4]
71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32AA [auth A5],
GD [auth D5]
60Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33BA [auth A6],
HD [auth D6]
54Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34CA [auth A7],
ID [auth D7]
49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35DA [auth A8],
JD [auth D8]
65Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2EB [auth CE],
FA [auth BE]
256Thermus thermophilus HB8Mutation(s): 0 
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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]
209Thermus 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 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7JB [auth CJ],
KA [auth BJ]
156Thermus thermophilus HB8Mutation(s): 0 
UniProt
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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 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11NB [auth CN],
OA [auth BN]
129Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12OB [auth CO],
PA [auth BO]
132Thermus thermophilus HB8Mutation(s): 0 
UniProt
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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 S14 type ZQB [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 
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Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16SB [auth CS],
TA [auth BS]
88Thermus thermophilus HB8Mutation(s): 0 
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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 
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Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19VB [auth CV],
WA [auth BV]
93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20WB [auth CW],
XA [auth BW]
106Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxXB [auth CX],
YA [auth BX]
27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7/L12JC [auth DI],
NC [auth DJ]
125Thermus thermophilusMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10LC [auth DY]173Thermus thermophilusMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11MC [auth DL]147Thermus thermophilusMutation(s): 0 
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BID [auth CG]
FAH [auth D4]
PJD [auth CQ]
SAB [auth A4]
SCC [auth BQ]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AAA [auth AA]
AAB [auth AT]
AAC [auth BA]
AAD [auth CA]
AAE [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.46α = 90
b = 446.2β = 90
c = 623.05γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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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: 2017-05-31
    Changes: Other
  • Version 2.0: 2019-07-03
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary