4V4I

Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.348 
  • R-Value Observed: 0.349 

wwPDB Validation 3D Report Full Report



Literature

Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements

Korostelev, A.Trakhanov, S.Laurberg, M.Noller, H.F.

(2006) Cell 126: 1065-1077

  • DOI: 10.1016/j.cell.2006.08.032
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Our understanding of the mechanism of protein synthesis has undergone rapid progress in recent years as a result of low-resolution X-ray and cryo-EM structures of ribosome functional complexes and high-resolution structures of ribosomal subunits and ...

    Our understanding of the mechanism of protein synthesis has undergone rapid progress in recent years as a result of low-resolution X-ray and cryo-EM structures of ribosome functional complexes and high-resolution structures of ribosomal subunits and vacant ribosomes. Here, we present the crystal structure of the Thermus thermophilus 70S ribosome containing a model mRNA and two tRNAs at 3.7 A resolution. Many structural details of the interactions between the ribosome, tRNA, and mRNA in the P and E sites and the ways in which tRNA structure is distorted by its interactions with the ribosome are seen. Differences between the conformations of vacant and tRNA-bound 70S ribosomes suggest an induced fit of the ribosome structure in response to tRNA binding, including significant changes in the peptidyl-transferase catalytic site.


    Organizational Affiliation

    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1A229Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplATT_C1739
Find proteins for Q72GV9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3C206Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplCTT_C1328
Find proteins for Q72I04 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13H163Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplMTT_C1101
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15J150Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplOTT_C1309
Find proteins for Q72I23 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17L118Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplQTT_C1299
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20O118Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplTTT_C0185
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22Q113Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplVTT_C1323
Find proteins for Q72I09 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24S110Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplXTT_C1317
Find proteins for Q72I15 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30X60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmDTT_C1310
Find proteins for Q72I22 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32Y60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmFrpl32TT_C0050
Find proteins for P62652 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34Z49Thermus thermophilus HB27Mutation(s): 0 
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35a65Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmITT_C0184
Find proteins for Q72L77 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36b37Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmJTT_C1304
Find proteins for Q72I28 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2c256Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsBrps2TT_C0509
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4e209Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsDrps4TT_C1301
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6g101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsFrps6TT_C1740
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9j128Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsIrps9TT_C1100
Find proteins for P62669 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15p89Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsOrps15TT_C0773
Find proteins for P62657 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17r105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsQrps17TT_C1319
Find proteins for P62658 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thxv27Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsUTT_C1030
Find proteins for P62613 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14I122Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplNTT_C1318
Find proteins for Q72I14 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16K141Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplPTT_C1321
Find proteins for Q72I11 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18M112Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplRTT_C1312
Find proteins for Q72I20 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19N146Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplSTT_C0669
Find proteins for Q72JU9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21P101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplUTT_C1424
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23R96Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplWTT_C1326
Find proteins for Q72I06 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25T206Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplYctcTT_C1225
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27U85Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmATT_C1423
Find proteins for Q72HR3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28V98Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmBTT_C1964
Find proteins for Q72G84 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29W72Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmCTT_C1320
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3d239Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsCrps3TT_C1322
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5f162Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsErps5TT_C1311
Find proteins for P62665 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2B276Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplBTT_C1325
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7h156Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsGrps7TT_C1332
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8i138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsHrps8TT_C1314
Find proteins for P62668 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10k105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsJrps10TT_C1329
Find proteins for P62653 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11l129Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsKrps11TT_C1302
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12m132Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsLrps12TT_C1333
Find proteins for P61941 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13n126Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsMrps13TT_C1303
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14o61Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsZrps14rpsNTT_C1315
Find proteins for P62656 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16q88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsPrps16TT_C0673
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18s88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsRrps18TT_C1742
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19t93Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsSrps19TT_C1324
Find proteins for P62660 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20u106Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsTrps20TT_C1031
Find proteins for P62661 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4D205Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplDTT_C1327
Find proteins for Q72I05 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5E182Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplETT_C1316
Find proteins for Q72I16 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6F180Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplFTT_C1313
Find proteins for Q72I19 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9G148Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplITT_C1743
Find proteins for Q72GV5 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 1
MoleculeChainsLengthOrganism
23S LARGE SUBUNIT RIBOSOMAL RNAw2889Thermus thermophilus HB27

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Entity ID: 32
MoleculeChainsLengthOrganism
P-site PHE-tRNAz76Escherichia coli

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Entity ID: 33
MoleculeChainsLengthOrganism
E-TRNA076Thermus thermophilus HB27

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Entity ID: 2
MoleculeChainsLengthOrganism
5S LARGE SUBUNIT RIBOSOMAL RNAx121Thermus thermophilus HB27

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Entity ID: 31
MoleculeChainsLengthOrganism
16S SMALL SUBUNIT RIBOSOMAL RNAy1522Thermus thermophilus HB27
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Entity ID: 34
MoleculeChainsLengthOrganism
MRNA110N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.348 
  • R-Value Observed: 0.349 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 507.81α = 90
b = 507.81β = 90
c = 689.52γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
CNSrefinement
d*TREKdata reduction
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 2.0: 2019-07-03
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary