4V8U

Crystal Structure of 70S Ribosome with Both Cognate tRNAs in the E and P Sites Representing an Authentic Elongation Complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of 70S ribosome with both cognate tRNAs in the E and P sites representing an authentic elongation complex.

Feng, S.Chen, Y.Gao, Y.G.

(2013) PLoS One 8: e58829-e58829

  • DOI: 10.1371/journal.pone.0058829
  • Primary Citation of Related Structures:  
    4V8U

  • PubMed Abstract: 
  • During the translation cycle, a cognate deacylated tRNA can only move together with the codon into the E site. We here present the first structure of a cognate tRNA bound to the ribosomal E site resulting from translocation by EF-G, in which an entire L1 stalk (L1 protein and L1 rRNA) interacts with E-site tRNA (E-tRNA), representing an authentic ribosome elongation complex ...

    During the translation cycle, a cognate deacylated tRNA can only move together with the codon into the E site. We here present the first structure of a cognate tRNA bound to the ribosomal E site resulting from translocation by EF-G, in which an entire L1 stalk (L1 protein and L1 rRNA) interacts with E-site tRNA (E-tRNA), representing an authentic ribosome elongation complex. Our results revealed that the Watson-Crick base pairing is formed at the first and second codon-anticodon positions in the E site in the ribosome elongation complex, whereas the codon-anticodon interaction in the third position is indirect. Analysis of the observed conformations of mRNA and E-tRNA suggests that the ribosome intrinsically has the potential to form codon-anticodon interaction in the E site, independently of the mRNA configuration. We also present a detailed description of the biologically relevant position of the entire L1 stalk and its interacting cognate E-tRNA, which provides a better understanding of the structural basis for translation elongation. Furthermore, to gain insight into translocation, we report the positioning of protein L6 contacting EF-G, as well as the conformational change of the C-terminal tail of protein S13 in the decoding center.


    Organizational Affiliation

    School of Biological Science, Nanyang Technological University, Singapore.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2 ABCB256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 3
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30S RIBOSOMAL PROTEIN S3 ACCC239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 4
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30S RIBOSOMAL PROTEIN S4 ADCD209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 5
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30S RIBOSOMAL PROTEIN S5 AECE162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 6
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30S RIBOSOMAL PROTEIN S6 AFCF101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
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30S RIBOSOMAL PROTEIN S7 AGCG156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 8
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30S RIBOSOMAL PROTEIN S8 AHCH138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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30S RIBOSOMAL PROTEIN S9 AICI128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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30S RIBOSOMAL PROTEIN S10 AJCJ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
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30S RIBOSOMAL PROTEIN S11 AKCK129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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30S RIBOSOMAL PROTEIN S12 ALCL132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
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30S RIBOSOMAL PROTEIN S13 AMCM126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
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30S RIBOSOMAL PROTEIN S14 TYPE Z ANCN61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
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30S RIBOSOMAL PROTEIN S15 AOCO89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
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30S RIBOSOMAL PROTEIN S16 APCP88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
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30S RIBOSOMAL PROTEIN S17 AQCQ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 18
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30S RIBOSOMAL PROTEIN S18 ARCR88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
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30S RIBOSOMAL PROTEIN S19 ASCS93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
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30S RIBOSOMAL PROTEIN S20 ATCT106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
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30S RIBOSOMAL PROTEIN THX AUCU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 25
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ELONGATION FACTOR G AYCY691Thermus thermophilus HB8Mutation(s): 0 
Gene Names: fusAfusTTHA1695
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Entity ID: 26
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50S RIBOSOMAL PROTEIN L27 B0D085Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 27
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50S RIBOSOMAL PROTEIN L28 B1D198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 28
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50S RIBOSOMAL PROTEIN L29 B2D272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 29
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50S RIBOSOMAL PROTEIN L30 B3D360Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 30
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50S RIBOSOMAL PROTEIN L31 B4D471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 31
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50S RIBOSOMAL PROTEIN L32 B5D560Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 32
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50S RIBOSOMAL PROTEIN L33 B6D654Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 33
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50S RIBOSOMAL PROTEIN L34 B7D749Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 34
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50S RIBOSOMAL PROTEIN L35 B8D865Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 35
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50S RIBOSOMAL PROTEIN L36 B9D937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 38
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50S RIBOSOMAL PROTEIN L1 BCDC229Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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Entity ID: 39
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50S RIBOSOMAL PROTEIN L2 BDDD276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 40
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50S RIBOSOMAL PROTEIN L3 BEDE206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 41
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50S RIBOSOMAL PROTEIN L4 BFDF210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 42
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50S RIBOSOMAL PROTEIN L5 BGDG182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 43
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50S RIBOSOMAL PROTEIN L6 BHDH180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 44
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50S RIBOSOMAL PROTEIN L10 BJDJ173Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
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50S RIBOSOMAL PROTEIN L13 BNDN140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 46
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50S RIBOSOMAL PROTEIN L14 BODO122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 47
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50S RIBOSOMAL PROTEIN L15 BPDP150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 48
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50S RIBOSOMAL PROTEIN L16 BQDQ141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 49
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50S RIBOSOMAL PROTEIN L17 BRDR118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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50S RIBOSOMAL PROTEIN L18 BSDS112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 51
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50S RIBOSOMAL PROTEIN L19 BTDT146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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50S RIBOSOMAL PROTEIN L20 BUDU118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 53
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50S RIBOSOMAL PROTEIN L21 BVDV101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 54
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50S RIBOSOMAL PROTEIN L22 BWDW113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 55
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50S RIBOSOMAL PROTEIN L23 BXDX96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 56
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50S RIBOSOMAL PROTEIN L24 BYDY110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 57
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50S RIBOSOMAL PROTEIN L25 BZDZ206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 1
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16S RIBOSOMAL RNAAA, CA1522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganismImage
MRNAAV, CV76Thermus thermophilus HB8
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Entity ID: 23
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RNAAW, CW77Thermus thermophilus HB8
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Entity ID: 24
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RNAAX, CX25Thermus thermophilus HB8
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Entity ID: 36
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23S RIBOSOMAL RNABA, DA2915Thermus thermophilus HB8
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Entity ID: 37
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5S RIBOSOMAL RNABB, DB122Thermus thermophilus HB8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 291.357α = 90
b = 269.425β = 91.78
c = 401.947γ = 90
Software Package:
Software NamePurpose
PHASERmodel building
CNSrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2018-04-18
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2019-06-12
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations