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


This is version 2.1 of the entry. See complete history


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: https://doi.org/10.1016/j.cell.2006.08.032
  • Primary Citation of Related Structures:  
    4V4I

  • 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 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1C [auth A]229Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth B]276Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth C]206Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth D]205Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth E]182Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth F]180Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9I [auth G]148Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13J [auth H]163Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14K [auth I]122Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15L [auth J]150Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16M [auth K]141Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17N [auth L]118Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18O [auth M]112Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19P [auth N]146Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20Q [auth O]118Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21R [auth P]101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22S [auth Q]113Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23T [auth R]96Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24U [auth S]110Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25V [auth T]206Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27W [auth U]85Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28X [auth V]98Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Y [auth W]72Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Z [auth X]60Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth Y]60Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth Z]49Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CA [auth a]65Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth b]37Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2IA [auth c]256Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3JA [auth d]239Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4KA [auth e]209Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5LA [auth f]162Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6MA [auth g]101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7NA [auth h]156Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8OA [auth i]138Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9PA [auth j]128Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10QA [auth k]105Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11RA [auth l]129Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12SA [auth m]132Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13TA [auth n]126Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14UA [auth o]61Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15VA [auth p]89Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16WA [auth q]88Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17XA [auth r]105Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P0DOY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18YA [auth s]88Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19ZA [auth t]93Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20AB [auth u]106Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxBB [auth v]27Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S LARGE SUBUNIT RIBOSOMAL RNAA [auth w]2,889Thermus thermophilus HB27
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S LARGE SUBUNIT RIBOSOMAL RNAB [auth x]121Thermus thermophilus HB27
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Entity ID: 31
MoleculeChains LengthOrganismImage
16S SMALL SUBUNIT RIBOSOMAL RNAEA [auth y]1,522Thermus thermophilus HB27
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Entity ID: 32
MoleculeChains LengthOrganismImage
P-site PHE-tRNAFA [auth z]76Escherichia coli
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Entity ID: 33
MoleculeChains LengthOrganismImage
E-TRNAGA [auth 0]76Thermus thermophilus HB27
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Entity ID: 34
MoleculeChains LengthOrganismImage
MRNAHA [auth 1]10N/A
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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  (Full details and data files)

  • 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
  • Version 2.1: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description