4V4R

Crystal structure of the whole ribosomal complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.90 Å
  • R-Value Free: 0.371 
  • R-Value Work: 0.351 
  • R-Value Observed: 0.353 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structures of the Ribosome in Complex with Release Factors RF1 and RF2 Bound to a Cognate Stop Codon.

Petry, S.Brodersen, D.E.Murphy IV, F.V.Dunham, C.M.Selmer, M.Tarry, M.J.Kelley, A.C.Ramakrishnan, V.

(2005) Cell 123: 1255-1266

  • DOI: 10.1016/j.cell.2005.09.039
  • Primary Citation of Related Structures:  
    4V4R, 4V4S, 4V4T

  • PubMed Abstract: 
  • During protein synthesis, translational release factors catalyze the release of the polypeptide chain when a stop codon on the mRNA reaches the A site of the ribosome. The detailed mechanism of this process is currently unknown. We present here the crystal structures of the ribosome from Thermus thermophilus with RF1 and RF2 bound to their cognate stop codons, at resolutions of 5 ...

    During protein synthesis, translational release factors catalyze the release of the polypeptide chain when a stop codon on the mRNA reaches the A site of the ribosome. The detailed mechanism of this process is currently unknown. We present here the crystal structures of the ribosome from Thermus thermophilus with RF1 and RF2 bound to their cognate stop codons, at resolutions of 5.9 Angstrom and 6.7 Angstrom, respectively. The structures reveal details of interactions of the factors with the ribosome and mRNA, including elements previously implicated in decoding and peptide release. They also shed light on conformational changes both in the factors and in the ribosome during termination. Differences seen in the interaction of RF1 and RF2 with the L11 region of the ribosome allow us to rationalize previous biochemical data. Finally, this work demonstrates the feasibility of crystallizing ribosomes with bound factors at a defined state along the translational pathway.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2E [auth AB]256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3F [auth AC]239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4G [auth AD]209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5H [auth AE]162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6I [auth AF]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7J [auth AG]156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8K [auth AH]138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9L [auth AI]128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10M [auth AJ]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11N [auth AK]129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12O [auth AL]135Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13P [auth AM]126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14Q [auth AN]61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15R [auth AO]89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16S [auth AP]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17T [auth AQ]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 21
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30S ribosomal protein S18U [auth AR]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19V [auth AS]93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20W [auth AT]106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxX [auth AU]27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide chain release factor 1Y [auth AY]354Thermus thermophilus HB8Mutation(s): 0 
Gene Names: prfATTHA1940
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2BA [auth BD]173Thermus thermophilusMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L3CA [auth BE]338Thermus thermophilusMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L4DA [auth BF]246Thermus thermophilusMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L5EA [auth BG]176Thermus thermophilusMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6FA [auth BH]177Thermus thermophilusMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L9GA [auth BI]149Thermus thermophilusMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13HA [auth BN]145Thermus thermophilusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14IA [auth BO]122Thermus thermophilusMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15JA [auth BP]164Thermus thermophilusMutation(s): 0 
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Entity ID: 37
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50S ribosomal protein L16KA [auth BQ]138Thermus thermophilusMutation(s): 0 
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Entity ID: 38
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50S ribosomal protein L18LA [auth BS]186Thermus thermophilusMutation(s): 0 
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Entity ID: 39
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50S ribosomal protein L19MA [auth BT]66Thermus thermophilusMutation(s): 0 
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Entity ID: 40
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50S ribosomal protein L22NA [auth BW]113Thermus thermophilusMutation(s): 0 
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Entity ID: 41
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50S ribosomal protein L23OA [auth BX]84Thermus thermophilusMutation(s): 0 
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Entity ID: 42
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50S ribosomal protein 24PA [auth BY]119Thermus thermophilusMutation(s): 0 
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Entity ID: 43
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50S ribosomal protein CTCQA [auth BZ]253Thermus thermophilusMutation(s): 0 
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Entity ID: 44
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50S ribosomal protein L17RA [auth BR]118Thermus thermophilusMutation(s): 0 
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Entity ID: 45
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50S ribosomal protein L20SA [auth BU]118Thermus thermophilusMutation(s): 0 
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Entity ID: 46
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50S ribosomal protein L21TA [auth BV]100Thermus thermophilusMutation(s): 0 
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Entity ID: 47
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50S ribosomal protein L29UA [auth B2]70Thermus thermophilusMutation(s): 0 
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Entity ID: 48
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50S ribosomal protein L30VA [auth B3]60Thermus thermophilusMutation(s): 0 
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Entity ID: 49
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50S ribosomal protein L27WA [auth B0]91Thermus thermophilusMutation(s): 0 
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Entity ID: 50
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50S ribosomal protein L31XA [auth B4]73Thermus thermophilusMutation(s): 0 
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Entity ID: 51
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50S ribosomal protein L32YA [auth B5]60Thermus thermophilusMutation(s): 0 
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Find proteins for P49228 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 52
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50S ribosomal protein L33ZA [auth B6]82Thermus thermophilusMutation(s): 0 
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Entity ID: 53
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50S ribosomal protein L34AB [auth B7]47Thermus thermophilusMutation(s): 0 
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Entity ID: 54
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50S ribosomal protein L35BB [auth B8]64Thermus thermophilusMutation(s): 0 
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Entity ID: 55
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50S ribosomal protein L36CB [auth B9]36Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q9RSK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 56
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50S ribosomal protein L11DB [auth BK]141Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P29395 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
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Entity ID: 1
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16S ribosomal RNAA [auth AA]1522Thermus thermophilus HB8
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Entity ID: 2
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P-site tRNA (Phe)B [auth AV]76Escherichia coli
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Entity ID: 3
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E-site tRNA (Phe)C [auth AW]76Escherichia coli
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  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    5'-R(*AP*UP*GP*UP*UP*CP*UP*AP*GP*UP*AP*CP*AP*AP*UP*AP*AP*U)-3'D [auth AX]18N/A
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    • Reference Sequence
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 26
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNAZ [auth BB]123Thermus thermophilus
    Protein Feature View
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    • Reference Sequence
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    Entity ID: 27
    MoleculeChainsLengthOrganismImage
    23S ribosomal RNAAA [auth BA]2916Thermus thermophilus HB8
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 5.90 Å
    • R-Value Free: 0.371 
    • R-Value Work: 0.351 
    • R-Value Observed: 0.353 
    • Space Group: P 43 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 518.993α = 90
    b = 518.993β = 90
    c = 365.139γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    CNSrefinement
    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