4V5E

Insights into translational termination from the structure of RF2 bound to the ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights Into Translational Termination from the Structure of Rf2 Bound to the Ribosome.

Weixlbaumer, A.Jin, H.Neubauer, C.Voorhees, R.M.Petry, S.Kelley, A.C.Ramakrishnan, V.

(2008) Science 322: 953-956

  • DOI: 10.1126/science.1164840
  • Primary Citation of Related Structures:  
    4V5E

  • PubMed Abstract: 
  • The termination of protein synthesis occurs through the specific recognition of a stop codon in the A site of the ribosome by a release factor (RF), which then catalyzes the hydrolysis of the nascent protein chain from the P-site transfer RNA. Here we pr ...

    The termination of protein synthesis occurs through the specific recognition of a stop codon in the A site of the ribosome by a release factor (RF), which then catalyzes the hydrolysis of the nascent protein chain from the P-site transfer RNA. Here we present, at a resolution of 3.5 angstroms, the crystal structure of RF2 in complex with its cognate UGA stop codon in the 70S ribosome. The structure provides insight into how RF2 specifically recognizes the stop codon; it also suggests a model for the role of a universally conserved GGQ motif in the catalysis of peptide release.


    Organizational Affiliation

    Medical Research Council (MRC) Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.



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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30S RIBOSOMAL PROTEIN S11 AKCK129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
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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 
Gene Names: rpsZrpsNTTHA1679
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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: 24
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDE CHAIN RELEASE FACTOR 2 AYCY351Thermus thermophilus HB8Mutation(s): 0 
Gene Names: prfBTTHA0142
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Entity ID: 25
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50S RIBOSOMAL PROTEIN L27 B0D085Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 26
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50S RIBOSOMAL PROTEIN L28 B1D198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 27
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50S RIBOSOMAL PROTEIN L29 B2D272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 28
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50S RIBOSOMAL PROTEIN L30 B3D360Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 29
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50S RIBOSOMAL PROTEIN L31 B4D471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 30
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50S RIBOSOMAL PROTEIN L32 B5D560Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 31
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50S RIBOSOMAL PROTEIN L33 B6D654Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 32
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50S RIBOSOMAL PROTEIN L34 B7D749Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 33
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50S RIBOSOMAL PROTEIN L35 B8D865Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 34
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50S RIBOSOMAL PROTEIN L36 B9D937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 37
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50S RIBOSOMAL PROTEIN L1 BCDC229Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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Entity ID: 38
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50S RIBOSOMAL PROTEIN L2 BDDD276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 39
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50S RIBOSOMAL PROTEIN L3 BEDE206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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50S RIBOSOMAL PROTEIN L4 BFDF210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 41
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50S RIBOSOMAL PROTEIN L5 BGDG182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 42
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50S RIBOSOMAL PROTEIN L6 BHDH180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 43
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50S RIBOSOMAL PROTEIN L9 BI148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
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50S RIBOSOMAL PROTEIN L10 BJDJ130Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
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50S RIBOSOMAL PROTEIN L11 BKDK147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplKTTHA0247
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Entity ID: 46
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50S RIBOSOMAL PROTEIN L13 BNDN140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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50S RIBOSOMAL PROTEIN L14 BODO122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 48
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50S RIBOSOMAL PROTEIN L15 BPDP150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 49
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50S RIBOSOMAL PROTEIN L16 BQDQ141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 50
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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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50S RIBOSOMAL PROTEIN L19 BTDT146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 53
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50S RIBOSOMAL PROTEIN L20 BUDU118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 54
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50S RIBOSOMAL PROTEIN L21 BVDV101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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50S RIBOSOMAL PROTEIN L22 BWDW113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 56
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50S RIBOSOMAL PROTEIN L23 BXDX96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 57
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50S RIBOSOMAL PROTEIN L24 BYDY110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25 BZDZ206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SHZ1
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  • Reference Sequence
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L9 DI148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SLQ1
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAAA, CA1522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganismImage
E-SITE TRNA PHE OR P-SITE TRNA PHE (UNMODIFIED BASES)AV, AW, CV, CW76Escherichia coli K-12
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  • Entity ID: 23
    MoleculeChainsLengthOrganismImage
    MRNAAX, CX8synthetic construct
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    Entity ID: 35
    MoleculeChainsLengthOrganismImage
    23S RIBOSOMAL RNABA, DA2901Thermus thermophilus HB8
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    Entity ID: 36
    MoleculeChainsLengthOrganismImage
    5S RIBOSOMAL RNABB, DB122Thermus thermophilus HB8
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    AD, AN, B9, CD, CN, D9
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AA, AE, AL, AM, AV, AW, AY, B1, B3, B5, B7, BA, BB, BC, BD, BF, BH, BP, BQ, BS, BU, CA, CL, CN, CV, CW, CY, D1, D3, D5, D7, DA, DB, DC, DD, DF, DH, DQ, DR, DU, DX, DY
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.45 Å
    • R-Value Free: 0.257 
    • R-Value Work: 0.210 
    • R-Value Observed: 0.210 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 211.341α = 90
    b = 450.908β = 90
    c = 614.01γ = 90
    Software Package:
    Software NamePurpose
    CNSmodel building
    CNSrefinement
    XDSdata reduction
    XSCALEdata 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 1.2: 2018-03-14
      Changes: Database references, Source and taxonomy, Structure summary