4WQF

Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation factor G and fusidic acid in the post-translocational state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation.

Lin, J.Gagnon, M.G.Bulkley, D.Steitz, T.A.

(2015) Cell 160: 219-227

  • DOI: 10.1016/j.cell.2014.11.049
  • Primary Citation of Related Structures:  
    4WQF, 4WPO, 4WQY, 4WQU

  • PubMed Abstract: 
  • The universally conserved GTPase elongation factor G (EF-G) catalyzes the translocation of tRNA and mRNA on the ribosome after peptide bond formation. Despite numerous studies suggesting that EF-G undergoes extensive conformational rearrangements during translocation, high-resolution structures exist for essentially only one conformation of EF-G in complex with the ribosome ...

    The universally conserved GTPase elongation factor G (EF-G) catalyzes the translocation of tRNA and mRNA on the ribosome after peptide bond formation. Despite numerous studies suggesting that EF-G undergoes extensive conformational rearrangements during translocation, high-resolution structures exist for essentially only one conformation of EF-G in complex with the ribosome. Here, we report four atomic-resolution crystal structures of EF-G bound to the ribosome programmed in the pre- and posttranslocational states and to the ribosome trapped by the antibiotic dityromycin. We observe a previously unseen conformation of EF-G in the pretranslocation complex, which is independently captured by dityromycin on the ribosome. Our structures provide insights into the conformational space that EF-G samples on the ribosome and reveal that tRNA translocation on the ribosome is facilitated by a structural transition of EF-G from a compact to an elongated conformation, which can be prevented by the antibiotic dityromycin.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA. Electronic address: thomas.steitz@yale.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1C [auth AC], IB [auth CC]228Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth AD], JB [auth CD]276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth AE], KB [auth CE]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth AF], LB [auth CF]210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth AG], MB [auth CG]182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth AH], NB [auth CH]180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10I [auth AK], OB [auth CK]173Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplJTTHA0209
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11J [auth AL], PB [auth CL]147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplKTTHA0247
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Entity ID: 11
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50S ribosomal protein L13K [auth AN], QB [auth CN]140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14L [auth AO], RB [auth CO]122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 13
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50S ribosomal protein L15M [auth AP], SB [auth CP]150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16N [auth AQ], TB [auth CQ]141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17O [auth AR], UB [auth CR]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18P [auth AS], VB [auth CS]112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 17
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50S ribosomal protein L19Q [auth AT], WB [auth CT]146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 18
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50S ribosomal protein L20R [auth AU], XB [auth CU]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21S [auth AV], YB [auth CV]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22T [auth AW], ZB [auth CW]113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23U [auth AX], AC [auth CX]96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24V [auth AY], BC [auth CY]110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25W [auth AZ], CC [auth CZ]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27X [auth A0], DC [auth C0]85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28Y [auth A1], EC [auth C1]98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29Z [auth A2], FC [auth C2]72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30AA [auth A3], GC [auth C3]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31BA [auth A4], HC [auth C4]71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32CA [auth A5], IC [auth C5]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33DA [auth A6], JC [auth C6]54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34EA [auth A7], KC [auth C7]49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35FA [auth A8], LC [auth C8]65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36GA [auth A9], MC [auth C9]37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2IA [auth BB], OC [auth DB]256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3JA [auth BC], PC [auth DC]239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4KA [auth BD], QC [auth DD]209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5LA [auth BE], RC [auth DE]162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6MA [auth BF], SC [auth DF]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7NA [auth BG], TC [auth DG]156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 41
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30S ribosomal protein S8OA [auth BH], UC [auth DH]138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9PA [auth BI], VC [auth DI]128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10QA [auth BJ], WC [auth DJ]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11RA [auth BK], XC [auth DK]129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12SA [auth BL], YC [auth DL]132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 46
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30S ribosomal protein S13TA [auth BM], ZC [auth DM]126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 47
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30S ribosomal protein S14 type ZUA [auth BN], AD [auth DN]61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
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30S ribosomal protein S15VA [auth BO], BD [auth DO]89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 49
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30S ribosomal protein S16WA [auth BP], CD [auth DP]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 50
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30S ribosomal protein S17XA [auth BQ], DD [auth DQ]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 51
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30S ribosomal protein S18YA [auth BR], ED [auth DR]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19ZA [auth BS], FD [auth DS]93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20AB [auth BT], GD [auth DT]106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
UniProt
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxBB [auth BU], HD [auth DU]27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9,Elongation factor GFB [auth BZ], LD [auth DZ]758Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242fusAfusTTHA1695
UniProt
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Find proteins for Q5SHN5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S Ribosomal RNAA [auth AA], GB [auth CA]2915Thermus thermophilus HB8
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S Ribosomal RNAB [auth AB], HB [auth CB]121Thermus thermophilus HB8
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Entity ID: 34
MoleculeChainsLengthOrganismImage
16S Ribosomal RNAHA [auth BA], NC [auth DA]1521Thermus thermophilus HB8
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  • Entity ID: 55
    MoleculeChainsLengthOrganismImage
    mRNACB [auth BV], ID [auth DV]18synthetic construct
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    Entity ID: 56
    MoleculeChainsLengthOrganismImage
    P-site tRNADB [auth BW], EB [auth BY], JD [auth DW], KD [auth DY]76Escherichia coli str. K-12 substr. MC4100
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    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    FUA
    Query on FUA

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    OEC [auth DZ], WVA [auth BZ]FUSIDIC ACID
    C31 H48 O6
    IECPWNUMDGFDKC-MZJAQBGESA-N
     Ligand Interaction
    GDP
    Query on GDP

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    PEC [auth DZ], XVA [auth BZ]GUANOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O11 P2
    QGWNDRXFNXRZMB-UUOKFMHZSA-N
     Ligand Interaction
    SF4
    Query on SF4

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    AEC [auth DD], EVA [auth BD]IRON/SULFUR CLUSTER
    Fe4 S4
    LJBDFODJNLIPKO-VKOJMFJBAC
     Ligand Interaction
    ZN
    Query on ZN

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    EMA [auth AY] , EXB [auth CY] , HEC [auth DN] , HXB [auth C4] , JXB [auth C5] , KXB [auth C6] , NMA [auth A4] , NVA [auth BN] , 
    EMA [auth AY],  EXB [auth CY],  HEC [auth DN],  HXB [auth C4],  JXB [auth C5],  KXB [auth C6],  NMA [auth A4],  NVA [auth BN],  NXB [auth C9],  PMA [auth A5],  SMA [auth A6],  YMA [auth A9]
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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