6GZ3

tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.

Flis, J.Holm, M.Rundlet, E.J.Loerke, J.Hilal, T.Dabrowski, M.Burger, J.Mielke, T.Blanchard, S.C.Spahn, C.M.T.Budkevich, T.V.

(2018) Cell Rep 25: 2676-2688.e7

  • DOI: 10.1016/j.celrep.2018.11.040
  • Primary Citation of Related Structures:  
    6GZ4, 6GZ3, 6GZ5

  • PubMed Abstract: 
  • Translocation moves the tRNA 2 ⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated ...

    Translocation moves the tRNA 2 ⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA 2 ⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. Electronic address: tetyana.budkevych@charite.de.



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Entity ID: 6
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ribosomal protein uS3F [auth BD]220Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
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Ribosomal protein S5G [auth BF]190Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 8
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ribosomal protein eS10H [auth BK]98Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S12I [auth BM]120Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS19J [auth BP]120Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
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ribosomal protein uS9K [auth BQ]139Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
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ribosomal protein eS17L [auth BR]125Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS13M [auth BS]139Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS19N [auth BT]143Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS10O [auth BU]97Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS25P [auth BZ]86Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S28Q [auth Bc]62Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS14R [auth Bd]51Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein RACK 1T [auth Bg]314Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS2U [auth BA]215Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S3aV [auth BB]212Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS5W [auth BC]222Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS4X [auth BE]257Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S6Y [auth BG]232Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S7Z [auth BH]183Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS8AA [auth BI]207Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S9 (Predicted)BA [auth BJ]179Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS15DA [auth BN]149Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS11EA [auth BO]136Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS21FA [auth BV]81Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S15aGA [auth BW]129Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S23HA [auth BX]141Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS24IA [auth BY]125Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS26JA [auth Ba]97Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS27KA [auth Bb]80Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS30LA [auth Be]55Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L8OA [auth AA]252Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL3PA [auth AB]394Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL4QA [auth AC]363Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL18RA [auth AD]294Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL6SA [auth AE]194Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL30TA [auth AF]234Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL8UA [auth AG]234Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL6VA [auth AH]191Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L10 (Predicted)WA [auth AI]211Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L11XA [auth AJ]169Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL13YA [auth AL]205Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL14ZA [auth AM]139Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL13BB [auth AO]195Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL22CB [auth AP]153Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL18DB [auth AQ]187Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL19EB [auth AR]181Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL20FB [auth AS]175Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL21GB [auth AT]157Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL22HB [auth AU]99Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L23IB [auth AV]129Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL24JB [auth AW]121Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL23KB [auth AX]117Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L26LB [auth AY]127Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L27MB [auth AZ]134Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL15NB [auth Aa]147Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL29OB [auth Ab]68Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL30PB [auth Ac]103Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL31QB [auth Ad]106Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL32RB [auth Ae]129Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL33SB [auth Af]109Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL34TB [auth Ag]114Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL29UB [auth Ah]122Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL36VB [auth Ai]97Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L37WB [auth Aj]84Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL38XB [auth Ak]69Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL39YB [auth Al]50Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL40ZB [auth Am]50Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL41AC [auth An]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
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ribosomal protein eL42BC [auth Ao]105Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL43CC [auth Ap]91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eL28DC [auth At]122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal proteinEC [auth Au]217Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SKZ8 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L12FC [auth Aq]151Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein uL10GC [auth AK]202Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetailsImage
eukaryotic elongation factor 2 (eEF2)HC [auth Ct]853Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
28S ribosomal RNAA [auth A2]3612Oryctolagus cuniculus
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Entity ID: 2
MoleculeChainsLengthOrganismImage
ap/P-site tRNAB [auth Bv]76Oryctolagus cuniculus
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  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    mRNAC [auth Bx]12Salmonella virus SP6
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    Entity ID: 4
    MoleculeChainsLengthOrganismImage
    pe/E-site-tRNAD [auth Bw]76Saccharomyces cerevisiae
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    Entity ID: 5
    MoleculeChainsLengthOrganismImage
    18S ribosomal RNAE [auth B1]1708Oryctolagus cuniculus
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    Entity ID: 39
    MoleculeChainsLengthOrganismImage
    5.8S ribosomal RNAMA [auth A3]157Oryctolagus cuniculus
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    Entity ID: 40
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNANA [auth A4]119Oryctolagus cuniculus
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GNP
    Query on GNP

    Download Ideal Coordinates CCD File 
    CP [auth Ct]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
    C10 H17 N6 O13 P3
    UQABYHGXWYXDTK-UUOKFMHZSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    AP [auth Ao], BO [auth Bd], BP [auth Ap], DO [auth Ba], XO [auth Aj]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AD [auth A2] , AE [auth A2] , AF [auth A2] , AG [auth A2] , AH [auth A2] , AI [auth A2] , AJ [auth A2] , AK [auth A2] , 
    AD [auth A2],  AE [auth A2],  AF [auth A2],  AG [auth A2],  AH [auth A2],  AI [auth A2],  AJ [auth A2],  AK [auth A2],  AL [auth A2],  AM [auth B1],  AN [auth B1],  AO [auth Bd],  BD [auth A2],  BE [auth A2],  BF [auth A2],  BG [auth A2],  BH [auth A2],  BI [auth A2],  BJ [auth A2],  BK [auth A2],  BL [auth A2],  BM [auth B1],  BN [auth B1],  CD [auth A2],  CE [auth A2],  CF [auth A2],  CG [auth A2],  CH [auth A2],  CI [auth A2],  CJ [auth A2],  CK [auth A2],  CL [auth A2],  CM [auth B1],  CN [auth B1],  CO [auth Ba],  DD [auth A2],  DE [auth A2],  DF [auth A2],  DG [auth A2],  DH [auth A2],  DI [auth A2],  DJ [auth A2],  DK [auth A2],  DL [auth A2],  DM [auth B1],  DN [auth B1],  ED [auth A2],  EE [auth A2],  EF [auth A2],  EG [auth A2],  EH [auth A2],  EI [auth A2],  EJ [auth A2],  EK [auth A2],  EL [auth Bx],  EM [auth B1],  EN [auth B1],  EO [auth A3],  FD [auth A2],  FE [auth A2],  FF [auth A2],  FG [auth A2],  FH [auth A2],  FI [auth A2],  FJ [auth A2],  FK [auth A2],  FL [auth Bx],  FM [auth B1],  FN [auth B1],  FO [auth A3],  GD [auth A2],  GE [auth A2],  GF [auth A2],  GG [auth A2],  GH [auth A2],  GI [auth A2],  GJ [auth A2],  GK [auth A2],  GL [auth B1],  GM [auth B1],  GN [auth B1],  GO [auth A3],  HD [auth A2],  HE [auth A2],  HF [auth A2],  HG [auth A2],  HH [auth A2],  HI [auth A2],  HJ [auth A2],  HK [auth A2],  HL [auth B1],  HM [auth B1],  HN [auth B1],  HO [auth A3],  IC [auth A2],  ID [auth A2],  IE [auth A2],  IF [auth A2],  IG [auth A2],  IH [auth A2],  II [auth A2],  IJ [auth A2],  IK [auth A2],  IL [auth B1],  IM [auth B1],  IN [auth B1],  IO [auth A3],  JC [auth A2],  JD [auth A2],  JE [auth A2],  JF [auth A2],  JG [auth A2],  JH [auth A2],  JI [auth A2],  JJ [auth A2],  JK [auth A2],  JL [auth B1],  JM [auth B1],  JN [auth B1],  JO [auth A3],  KC [auth A2],  KD [auth A2],  KE [auth A2],  KF [auth A2],  KG [auth A2],  KH [auth A2],  KI [auth A2],  KJ [auth A2],  KK [auth A2],  KL [auth B1],  KM [auth B1],  KN [auth B1],  KO [auth A4],  LC [auth A2],  LD [auth A2],  LE [auth A2],  LF [auth A2],  LG [auth A2],  LH [auth A2],  LI [auth A2],  LJ [auth A2],  LK [auth A2],  LL [auth B1],  LM [auth B1],  LN [auth B1],  LO [auth A4],  MC [auth A2],  MD [auth A2],  ME [auth A2],  MF [auth A2],  MG [auth A2],  MH [auth A2],  MI [auth A2],  MJ [auth A2],  MK [auth A2],  ML [auth B1],  MM [auth B1],  MN [auth B1],  MO [auth A4],  NC [auth A2],  ND [auth A2],  NE [auth A2],  NF [auth A2],  NG [auth A2],  NH [auth A2],  NI [auth A2],  NJ [auth A2],  NK [auth A2],  NL [auth B1],  NM [auth B1],  NN [auth B1],  NO [auth A4],  OC [auth A2],  OD [auth A2],  OE [auth A2],  OF [auth A2],  OG [auth A2],  OH [auth A2],  OI [auth A2],  OJ [auth A2],  OK [auth A2],  OL [auth B1],  OM [auth B1],  ON [auth B1],  OO [auth A4],  PC [auth A2],  PD [auth A2],  PE [auth A2],  PF [auth A2],  PG [auth A2],  PH [auth A2],  PI [auth A2],  PJ [auth A2],  PK [auth A2],  PL [auth B1],  PM [auth B1],  PN [auth B1],  PO [auth A4],  QC [auth A2],  QD [auth A2],  QE [auth A2],  QF [auth A2],  QG [auth A2],  QH [auth A2],  QI [auth A2],  QJ [auth A2],  QK [auth A2],  QL [auth B1],  QM [auth B1],  QN [auth B1],  QO [auth A4],  RC [auth A2],  RD [auth A2],  RE [auth A2],  RF [auth A2],  RG [auth A2],  RH [auth A2],  RI [auth A2],  RJ [auth A2],  RK [auth A2],  RL [auth B1],  RM [auth B1],  RN [auth B1],  RO [auth A4],  SC [auth A2],  SD [auth A2],  SE [auth A2],  SF [auth A2],  SG [auth A2],  SH [auth A2],  SI [auth A2],  SJ [auth A2],  SK [auth A2],  SL [auth B1],  SM [auth B1],  SN [auth B1],  SO [auth AA],  TC [auth A2],  TD [auth A2],  TE [auth A2],  TF [auth A2],  TG [auth A2],  TH [auth A2],  TI [auth A2],  TJ [auth A2],  TK [auth A2],  TL [auth B1],  TM [auth B1],  TN [auth B1],  TO [auth AL],  UC [auth A2],  UD [auth A2],  UE [auth A2],  UF [auth A2],  UG [auth A2],  UH [auth A2],  UI [auth A2],  UJ [auth A2],  UK [auth A2],  UL [auth B1],  UM [auth B1],  UN [auth B1],  UO [auth AN],  VC [auth A2],  VD [auth A2],  VE [auth A2],  VF [auth A2],  VG [auth A2],  VH [auth A2],  VI [auth A2],  VJ [auth A2],  VK [auth A2],  VL [auth B1],  VM [auth B1],  VN [auth B1],  VO [auth AP],  WC [auth A2],  WD [auth A2],  WE [auth A2],  WF [auth A2],  WG [auth A2],  WH [auth A2],  WI [auth A2],  WJ [auth A2],  WK [auth A2],  WL [auth B1],  WM [auth B1],  WN [auth B1],  WO [auth AY],  XC [auth A2],  XD [auth A2],  XE [auth A2],  XF [auth A2],  XG [auth A2],  XH [auth A2],  XI [auth A2],  XJ [auth A2],  XK [auth A2],  XL [auth B1],  XM [auth B1],  XN [auth BD],  YC [auth A2],  YD [auth A2],  YE [auth A2],  YF [auth A2],  YG [auth A2],  YH [auth A2],  YI [auth A2],  YJ [auth A2],  YK [auth A2],  YL [auth B1],  YM [auth B1],  YN [auth BD],  YO [auth Al],  ZC [auth A2],  ZD [auth A2],  ZE [auth A2],  ZF [auth A2],  ZG [auth A2],  ZH [auth A2],  ZI [auth A2],  ZJ [auth A2],  ZK [auth A2],  ZL [auth B1],  ZM [auth B1],  ZN [auth BS],  ZO [auth An]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    DDE
    Query on DDE
    HC [auth Ct]L-PEPTIDE LINKINGC13 H24 N5 O3HIS
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.60 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    German Research FoundationGermanyDFG SFB 740
    National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM079238
    National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM115327-Tan

    Revision History  (Full details and data files)

    • Version 1.0: 2018-12-05
      Type: Initial release
    • Version 1.1: 2018-12-19
      Changes: Data collection, Database references