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 AB, CB256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsB, rps2, TTHA0861
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3 AC, CC239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsC, rps3, TTHA1686
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4 AD, CD209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsD, rps4, TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5 AE, CE162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsE, TTHA1675
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6 AF, CF101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsF, TTHA0245
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7 AG, CG156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsG, rps7, TTHA1696
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8 AH, CH138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsH, TTHA1678
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9 AI, CI128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsI, rps9, TTHA1464
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10 AJ, CJ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJ, TTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11 AK, CK129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsK, rps11, TTHA1666
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Entity ID: 12
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30S RIBOSOMAL PROTEIN S12 AL, CL132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsL, TTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13 AM, CM126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsM, rps13, TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14 TYPE Z AN, CN61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZ, rpsN, TTHA1679
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15 AO, CO89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsO, TTHA1138
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16 AP, CP88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsP, TTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17 AQ, CQ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQ, TTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18 AR, CR88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsR, TTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19 AS, CS93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsS, TTHA1688
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20 AT, CT106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsT, rps20, TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THX AU, CU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsU, TTHA1396
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDE CHAIN RELEASE FACTOR 2 AY, CY351Thermus thermophilus HB8Mutation(s): 0 
Gene Names: prfB, TTHA0142
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27 B0, D085Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmA, TTHA1782
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28 B1, D198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmB, TTHA0042
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29 B2, D272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmC, TTHA1684
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30 B3, D360Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmD, TTHA1674
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31 B4, D471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmE, TTHA1073
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32 B5, D560Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmF, rpl32, TTHA0418
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33 B6, D654Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmG, rpl33, TTHA0250
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34 B7, D749Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmH, rpl34, TTHA0446
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35 B8, D865Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmI, TTHA0552
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L36 B9, D937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJ, TTHA1668
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L1 BC, DC229Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplA, TTHA0246
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2 BD, DD276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplB, TTHA1689
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3 BE, DE206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplC, TTHA1692
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4 BF, DF210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplD, TTHA1691
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Entity ID: 41
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50S RIBOSOMAL PROTEIN L5 BG, DG182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplE, TTHA1680
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Entity ID: 42
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50S RIBOSOMAL PROTEIN L6 BH, DH180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplF, TTHA1677
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 43
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50S RIBOSOMAL PROTEIN L9 BI148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplI, TTHA0242
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Entity ID: 44
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50S RIBOSOMAL PROTEIN L10 BJ, DJ130Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
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50S RIBOSOMAL PROTEIN L11 BK, DK147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplK, TTHA0247
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Entity ID: 46
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50S RIBOSOMAL PROTEIN L13 BN, DN140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplM, TTHA1465
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Entity ID: 47
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50S RIBOSOMAL PROTEIN L14 BO, DO122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplN, TTHA1682
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 48
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50S RIBOSOMAL PROTEIN L15 BP, DP150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplO, TTHA1673
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L16 BQ, DQ141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplP, TTHA1685
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Entity ID: 50
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50S RIBOSOMAL PROTEIN L17 BR, DR118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQ, rpl17, TTHA1663
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18 BS, DS112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplR, TTHA1676
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Entity ID: 52
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50S RIBOSOMAL PROTEIN L19 BT, DT146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplS, TTHA1031
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Entity ID: 53
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50S RIBOSOMAL PROTEIN L20 BU, DU118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplT, TTHA0553
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Entity ID: 54
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50S RIBOSOMAL PROTEIN L21 BV, DV101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplU, TTHA1783
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Entity ID: 55
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50S RIBOSOMAL PROTEIN L22 BW, DW113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplV, TTHA1687
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 56
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50S RIBOSOMAL PROTEIN L23 BX, DX96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplW, TTHA1690
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24 BY, DY110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplX, TTHA1681
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25 BZ, DZ206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplY, rpl25, rptL5, TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 59
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50S RIBOSOMAL PROTEIN L9 DI148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplI, TTHA0242
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAAA, CA1522Thermus thermophilus HB8
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Entity ID: 22
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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


    View more in-depth experimental data

    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