4V6C

Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of the ribosome in intermediate States of ratcheting.

Zhang, W.Dunkle, J.A.Cate, J.H.

(2009) Science 325: 1014-1017

  • DOI: 10.1126/science.1175275
  • Primary Citation of Related Structures:  
    4V6D, 4V6E, 4V6C

  • PubMed Abstract: 
  • Protein biosynthesis on the ribosome requires repeated cycles of ratcheting, which couples rotation of the two ribosomal subunits with respect to each other, and swiveling of the head domain of the small subunit. However, the molecular basis for how ...

    Protein biosynthesis on the ribosome requires repeated cycles of ratcheting, which couples rotation of the two ribosomal subunits with respect to each other, and swiveling of the head domain of the small subunit. However, the molecular basis for how the two ribosomal subunits rearrange contacts with each other during ratcheting while remaining stably associated is not known. Here, we describe x-ray crystal structures of the intact Escherichia coli ribosome, either in the apo-form (3.5 angstrom resolution) or with one (4.0 angstrom resolution) or two (4.0 angstrom resolution) anticodon stem-loop tRNA mimics bound, that reveal intermediate states of intersubunit rotation. In the structures, the interface between the small and large ribosomal subunits rearranges in discrete steps along the ratcheting pathway. Positioning of the head domain of the small subunit is controlled by interactions with the large subunit and with the tRNA bound in the peptidyl-tRNA site. The intermediates observed here provide insight into how tRNAs move into the hybrid state of binding that precedes the final steps of mRNA and tRNA translocation.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA.



Macromolecules

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Entity ID: 1
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30S ribosomal protein S2ABCB241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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30S ribosomal protein S3ACCC233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 3
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30S ribosomal protein S4ADCD206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 4
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30S ribosomal protein S5AECE167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 5
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30S ribosomal protein S6AFCF135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 6
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30S ribosomal protein S7AGCG179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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30S ribosomal protein S8AHCH130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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30S ribosomal protein S9AICI130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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30S ribosomal protein S10AJCJ103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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30S ribosomal protein S11AKCK129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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30S ribosomal protein S12ALCL124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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30S ribosomal protein S13AMCM118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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30S ribosomal protein S14ANCN101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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30S ribosomal protein S15AOCO89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 15
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30S ribosomal protein S16APCP82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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30S ribosomal protein S17AQCQ84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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30S ribosomal protein S18ARCR75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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30S ribosomal protein S19ASCS92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 19
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30S ribosomal protein S20ATCT87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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30S ribosomal protein S21AUCU71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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Entity ID: 24
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50S ribosomal protein L2BCDC273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 25
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50S ribosomal protein L3BDDD209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 26
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50S ribosomal protein L4BEDE201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 27
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50S ribosomal protein L5BFDF179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 28
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50S ribosomal protein L6BGDG177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 29
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50S ribosomal protein L9BHDH149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 30
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50S ribosomal protein L11BIDI142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 31
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50S ribosomal protein L13BJDJ142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 32
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50S ribosomal protein L14BKDK123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 33
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50S ribosomal protein L15BLDL144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 34
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50S ribosomal protein L16BMDM136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 35
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50S ribosomal protein L17BNDN127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 36
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50S ribosomal protein L18BODO117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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50S ribosomal protein L19BPDP115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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50S ribosomal protein L20BQDQ118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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50S ribosomal protein L21BRDR103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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50S ribosomal protein L22BSDS110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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50S ribosomal protein L23BTDT100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 42
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50S ribosomal protein L24BUDU104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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50S ribosomal protein L25BVDV94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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50S ribosomal protein L27BWDW85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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50S ribosomal protein L28BXDX78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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50S ribosomal protein L29BYDY63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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50S ribosomal protein L30BZDZ59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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50S ribosomal protein L32B0D057Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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50S ribosomal protein L33B1D155Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 50
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50S ribosomal protein L34B2D246Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 51
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50S ribosomal protein L35B3D365Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 52
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50S ribosomal protein L36B4D438Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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16S rRNAAA1533Escherichia coli
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23S rRNABA, DA2903Escherichia coli
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5S rRNABB118Escherichia coli
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16S rRNACA1530Escherichia coli
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5S rRNADB117Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
B4, D4
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AA, BA, BB, CA, DA, DB, DJ
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.887α = 90
b = 434.93β = 90
c = 622.921γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other