4V8O

Crystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.293 
  • R-Value Observed: 0.293 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the Hybrid State of Ribosome in Complex with the Guanosine Triphosphatase Release Factor 3.

Jin, H.Kelley, A.C.Ramakrishnan, V.

(2011) Proc Natl Acad Sci U S A 108: 15798

  • DOI: 10.1073/pnas.1112185108
  • Primary Citation of Related Structures:  
    4V8O

  • PubMed Abstract: 
  • Protein release factor 3 (RF3), a guanosine triphosphatase, binds to ribosome after release of the nascent peptide and promotes dissociation of the class I release factors during the termination of protein synthesis. Here we present the crystal structure of the 70S ribosome with RF3 in the presence of a nonhydrolyzable GTP analogue, guanosine 5'-β,γ-methylenetriphosphate (GDPCP), refined to 3 ...

    Protein release factor 3 (RF3), a guanosine triphosphatase, binds to ribosome after release of the nascent peptide and promotes dissociation of the class I release factors during the termination of protein synthesis. Here we present the crystal structure of the 70S ribosome with RF3 in the presence of a nonhydrolyzable GTP analogue, guanosine 5'-β,γ-methylenetriphosphate (GDPCP), refined to 3.8 Å resolution. The structure shows that the subunits of the ribosome are rotated relative to each other compared to the canonical state, resulting in a P/E hybrid state for the transfer RNA. The substantial conformational rearrangements in the complex are described and suggest how RF3, by stabilizing the hybrid state of the ribosome, facilitates the dissociation of class I release factors.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom. hjin@mrc-lmb.cam.ac.uk



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Entity ID: 2
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30S RIBOSOMAL PROTEIN S2B [auth AB]256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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30S RIBOSOMAL PROTEIN S3C [auth AC]239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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30S RIBOSOMAL PROTEIN S4D [auth AD]209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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30S RIBOSOMAL PROTEIN S5E [auth AE]162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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30S RIBOSOMAL PROTEIN S6F [auth AF]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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30S RIBOSOMAL PROTEIN S7G [auth AG]156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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30S RIBOSOMAL PROTEIN S8H [auth AH]138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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30S RIBOSOMAL PROTEIN S9I [auth AI]128Thermus thermophilus HB8Mutation(s): 0 
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30S RIBOSOMAL PROTEIN S10J [auth AJ]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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30S RIBOSOMAL PROTEIN S11K [auth AK]129Thermus thermophilus HB8Mutation(s): 0 
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30S RIBOSOMAL PROTEIN S12L [auth AL]135Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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30S RIBOSOMAL PROTEIN S13M [auth AM]126Thermus thermophilus HB8Mutation(s): 0 
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30S RIBOSOMAL PROTEIN S14 TYPE ZN [auth AN]61Thermus thermophilus HB8Mutation(s): 0 
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30S RIBOSOMAL PROTEIN S15O [auth AO]89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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30S RIBOSOMAL PROTEIN S16P [auth AP]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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30S RIBOSOMAL PROTEIN S17Q [auth AQ]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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30S RIBOSOMAL PROTEIN S18R [auth AR]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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30S RIBOSOMAL PROTEIN S19S [auth AS]93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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30S RIBOSOMAL PROTEIN S20T [auth AT]106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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30S RIBOSOMAL PROTEIN THXU [auth AU]27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 24
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PEPTIDE CHAIN RELEASE FACTOR 3X [auth AY]529Escherichia coli str. K-12 substr. DH10BMutation(s): 0 
Gene Names: prfCECDH10B_4532
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50S RIBOSOMAL PROTEIN L27Y [auth B0]85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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50S RIBOSOMAL PROTEIN L28Z [auth B1]98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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50S RIBOSOMAL PROTEIN L29AA [auth B2]72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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50S RIBOSOMAL PROTEIN L30BA [auth B3]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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50S RIBOSOMAL PROTEIN L31CA [auth B4]71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 30
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50S RIBOSOMAL PROTEIN L32DA [auth B5]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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50S RIBOSOMAL PROTEIN L33EA [auth B6]54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 32
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50S RIBOSOMAL PROTEIN L34FA [auth B7]49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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50S RIBOSOMAL PROTEIN L35GA [auth B8]65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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50S RIBOSOMAL PROTEIN L36HA [auth B9]37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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50S RIBOSOMAL PROTEIN L1KA [auth BC]229Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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50S RIBOSOMAL PROTEIN L2LA [auth BD]276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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50S RIBOSOMAL PROTEIN L3MA [auth BE]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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50S RIBOSOMAL PROTEIN L4NA [auth BF]210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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50S RIBOSOMAL PROTEIN L5OA [auth BG]182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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50S RIBOSOMAL PROTEIN L6PA [auth BH]180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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50S RIBOSOMAL PROTEIN L10QA [auth BJ]173Thermus thermophilus HB8Mutation(s): 0 
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50S RIBOSOMAL PROTEIN L11RA [auth BK]147Thermus thermophilus HB8Mutation(s): 0 
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50S RIBOSOMAL PROTEIN L13SA [auth BN]140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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50S RIBOSOMAL PROTEIN L14TA [auth BO]122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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50S RIBOSOMAL PROTEIN L15UA [auth BP]150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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50S RIBOSOMAL PROTEIN L16VA [auth BQ]141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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50S RIBOSOMAL PROTEIN L17WA [auth BR]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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50S RIBOSOMAL PROTEIN L18XA [auth BS]112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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50S RIBOSOMAL PROTEIN L19YA [auth BT]146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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50S RIBOSOMAL PROTEIN L20ZA [auth BU]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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50S RIBOSOMAL PROTEIN L21AB [auth BV]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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50S RIBOSOMAL PROTEIN L22BB [auth BW]113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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50S RIBOSOMAL PROTEIN L23CB [auth BX]96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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50S RIBOSOMAL PROTEIN L24DB [auth BY]110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25EB [auth BZ]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SHZ1 
Go to UniProtKB:  Q5SHZ1
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RRNAA [auth AA]1522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganismImage
PE HYBRID STATE TRNA FMETV [auth AV]77Escherichia coli K-12
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  • Entity ID: 23
    MoleculeChainsLengthOrganismImage
    MRNA 5'-R(*AP*AP*AP*AP*AP*AP*UP*GP*UP)-3'W [auth AX]9Escherichia coli
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    Entity ID: 35
    MoleculeChainsLengthOrganismImage
    23S RIBOSOMAL RNAIA [auth BA]2915Thermus thermophilus HB8
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    Entity ID: 36
    MoleculeChainsLengthOrganismImage
    5S RIBOSOMAL RNAJA [auth BB]122Thermus thermophilus HB8
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GCP
    Query on GCP

    Download Ideal Coordinates CCD File 
    FB [auth AY]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
    C11 H18 N5 O13 P3
    PHBDHXOBFUBCJD-KQYNXXCUSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.80 Å
    • R-Value Free: 0.351 
    • R-Value Work: 0.293 
    • R-Value Observed: 0.293 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 204.7α = 90
    b = 229.3β = 90.17
    c = 307γ = 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  (Full details and data files)

    • Version 1.0: 2014-07-09
      Type: Initial release
    • Version 1.1: 2014-12-10
      Changes: Other
    • Version 1.2: 2019-10-30
      Changes: Advisory, Data collection, Derived calculations