6R6P

Structure of XBP1u-paused ribosome nascent chain complex (rotated state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural and mutational analysis of the ribosome-arresting human XBP1u.

Shanmuganathan, V.Schiller, N.Magoulopoulou, A.Cheng, J.Braunger, K.Cymer, F.Berninghausen, O.Beatrix, B.Kohno, K.Heijne, G.V.Beckmann, R.

(2019) Elife 8

  • DOI: 10.7554/eLife.46267
  • Primary Citation of Related Structures:  
    6R5Q, 6R6P, 6R6G, 6R7Q

  • PubMed Abstract: 
  • XBP1u, a central component of the unfolded protein response (UPR), is a mammalian protein containing a functionally critical translational arrest peptide (AP). Here, we present a 3 Å cryo-EM structure of the stalled human XBP1u AP. It forms a unique turn in the ribosomal exit tunnel proximal to the peptidyl transferase center where it causes a subtle distortion, thereby explaining the temporary translational arrest induced by XBP1u ...

    XBP1u, a central component of the unfolded protein response (UPR), is a mammalian protein containing a functionally critical translational arrest peptide (AP). Here, we present a 3 Å cryo-EM structure of the stalled human XBP1u AP. It forms a unique turn in the ribosomal exit tunnel proximal to the peptidyl transferase center where it causes a subtle distortion, thereby explaining the temporary translational arrest induced by XBP1u. During ribosomal pausing the hydrophobic region 2 (HR2) of XBP1u is recognized by SRP, but fails to efficiently gate the Sec61 translocon. An exhaustive mutagenesis scan of the XBP1u AP revealed that only 8 out of 20 mutagenized positions are optimal; in the remaining 12 positions, we identify 55 different mutations increase the level of translational arrest. Thus, the wildtype XBP1u AP induces only an intermediate level of translational arrest, allowing efficient targeting by SRP without activating the Sec61 channel.


    Organizational Affiliation

    Gene Center, Department of Biochemistry, Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany.



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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
uL2D [auth A]244Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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uL3E [auth B]394Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
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Entity ID: 6
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uL4F [auth C]362Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L5G [auth D]292Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L6H [auth E]248Oryctolagus cuniculusMutation(s): 0 
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uL30I [auth F]225Oryctolagus cuniculusMutation(s): 0 
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eL8J [auth G]241Oryctolagus cuniculusMutation(s): 0 
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uL6K [auth H]190Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L10 (Predicted)L [auth I]213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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uL5M [auth J]169Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L13N [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L14O [auth M]138Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L15P [auth N]203Oryctolagus cuniculusMutation(s): 0 
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uL13Q [auth O]199Oryctolagus cuniculusMutation(s): 0 
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uL22R [auth P]153Oryctolagus cuniculusMutation(s): 0 
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eL18S [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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eL19T [auth R]180Oryctolagus cuniculusMutation(s): 0 
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eL20U [auth S]175Oryctolagus cuniculusMutation(s): 0 
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eL21V [auth T]159Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L22W [auth U]99Oryctolagus cuniculusMutation(s): 0 
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uL14X [auth V]131Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L24Y [auth W]63Oryctolagus cuniculusMutation(s): 0 
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uL23Z [auth X]119Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L26AA [auth Y]134Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L27BA [auth Z]135Oryctolagus cuniculusMutation(s): 0 
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uL15CA [auth a]147Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L29DA [auth b]75Oryctolagus cuniculusMutation(s): 0 
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eL30EA [auth c]94Oryctolagus cuniculusMutation(s): 0 
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eL31FA [auth d]107Oryctolagus cuniculusMutation(s): 0 
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eL32GA [auth e]128Oryctolagus cuniculusMutation(s): 0 
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eL33HA [auth f]109Oryctolagus cuniculusMutation(s): 0 
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eL34IA [auth g]114Oryctolagus cuniculusMutation(s): 0 
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uL29JA [auth h]122Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L36KA [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L37LA [auth j]86Oryctolagus cuniculusMutation(s): 0 
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eL38MA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL39NA [auth l]50Oryctolagus cuniculusMutation(s): 0 
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eL40OA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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60s ribosomal protein l41PA [auth n]23Oryctolagus cuniculusMutation(s): 0 
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eL42QA [auth o]104Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL43RA [auth p]91Oryctolagus cuniculusMutation(s): 0 
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eL28SA [auth r]125Oryctolagus cuniculusMutation(s): 0 
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60S acidic ribosomal protein P0TA [auth s]198Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L12UA [auth t]163Oryctolagus cuniculusMutation(s): 0 
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X-box-binding protein 1VA [auth 1]24Homo sapiensMutation(s): 0 
Gene Names: XBP1TREB5XBP2
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uS2ZA [auth q]217Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S3aAB [auth u]213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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40S ribosomal protein S4CB [auth x]262Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S6DB [auth z]237Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S7EB [auth y]189Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S8FB [auth CC]206Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S9 (Predicted)GB [auth XX]185Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Ribosomal protein S11HB [auth EE]151Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS15IB [auth QQ]149Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS13
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uS11JB [auth MM]136Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S16KB [auth UU]142Oryctolagus cuniculusMutation(s): 0 
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eS17LB [auth YY]132Oryctolagus cuniculusMutation(s): 0 
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eS21MB [auth HH]83Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S15aNB [auth TT]129Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S23OB [auth VV]141Oryctolagus cuniculusMutation(s): 0 
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eS24PB [auth NN]124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
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eS26QB [auth ZZ]101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
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40S ribosomal protein S27RB [auth JJ]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
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40S ribosomal protein S30SB [auth AA]55Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
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Ribosomal protein S3TB [auth DD]228Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 73
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Ribosomal protein S5UB [auth BB]191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 74
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eS10VB [auth SS]96Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
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40S ribosomal protein S12WB [auth RR]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
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uS14XB [auth 9]120Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
uS13YB [auth II]144Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
eS19ZB [auth PP]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
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uS10AC [auth GG]100Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
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ribosomal protein eS25BC [auth OO]75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
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Ribosomal protein S28CC [auth FF]62Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 82
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S29DC [auth w]55Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
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eS31EC [auth 0]68Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
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ribosomal protein RACK1FC [auth 6]313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
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28S ribosomal RNAA [auth 5]3662Oryctolagus cuniculus
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Entity ID: 2
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5S ribosomal RNAB [auth 7]120Oryctolagus cuniculus
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Entity ID: 3
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5.8S ribosomal RNAC [auth 8]156Oryctolagus cuniculus
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Entity ID: 49
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A/P-tRNAWA [auth 2]76Saccharomyces cerevisiae
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Entity ID: 50
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P/E-tRNAXA [auth 3]75Saccharomyces cerevisiae
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Entity ID: 51
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18S rRNAYA [auth K]1698Oryctolagus cuniculus
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  • Entity ID: 85
    MoleculeChainsLengthOrganismImage
    mRNAGC [auth 4]10Homo sapiens
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    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    JI [auth g], LI [auth j], MI [auth m], NI [auth o], OI [auth p]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AD [auth 5] , AE [auth 5] , AF [auth 5] , AG [auth 5] , AH [auth 5] , AI [auth 7] , BD [auth 5] , BE [auth 5] , 
    AD [auth 5],  AE [auth 5],  AF [auth 5],  AG [auth 5],  AH [auth 5],  AI [auth 7],  BD [auth 5],  BE [auth 5],  BF [auth 5],  BG [auth 5],  BH [auth 5],  BI [auth 7],  CD [auth 5],  CE [auth 5],  CF [auth 5],  CG [auth 5],  CH [auth 5],  CI [auth 7],  DD [auth 5],  DE [auth 5],  DF [auth 5],  DG [auth 5],  DH [auth 5],  DI [auth 8],  ED [auth 5],  EE [auth 5],  EF [auth 5],  EG [auth 5],  EH [auth 5],  EI [auth I],  FD [auth 5],  FE [auth 5],  FF [auth 5],  FG [auth 5],  FH [auth 5],  FI [auth P],  GD [auth 5],  GE [auth 5],  GF [auth 5],  GG [auth 5],  GH [auth 5],  GI [auth Q],  HC [auth 5],  HD [auth 5],  HE [auth 5],  HF [auth 5],  HG [auth 5],  HH [auth 5],  HI [auth V],  IC [auth 5],  ID [auth 5],  IE [auth 5],  IF [auth 5],  IG [auth 5],  IH [auth 5],  II [auth e],  JC [auth 5],  JD [auth 5],  JE [auth 5],  JF [auth 5],  JG [auth 5],  JH [auth 5],  KC [auth 5],  KD [auth 5],  KE [auth 5],  KF [auth 5],  KG [auth 5],  KH [auth 5],  KI [auth g],  LC [auth 5],  LD [auth 5],  LE [auth 5],  LF [auth 5],  LG [auth 5],  LH [auth 5],  MC [auth 5],  MD [auth 5],  ME [auth 5],  MF [auth 5],  MG [auth 5],  MH [auth 5],  NC [auth 5],  ND [auth 5],  NE [auth 5],  NF [auth 5],  NG [auth 5],  NH [auth 5],  OC [auth 5],  OD [auth 5],  OE [auth 5],  OF [auth 5],  OG [auth 5],  OH [auth 5],  PC [auth 5],  PD [auth 5],  PE [auth 5],  PF [auth 5],  PG [auth 5],  PH [auth 5],  QC [auth 5],  QD [auth 5],  QE [auth 5],  QF [auth 5],  QG [auth 5],  QH [auth 5],  RC [auth 5],  RD [auth 5],  RE [auth 5],  RF [auth 5],  RG [auth 5],  RH [auth 5],  SC [auth 5],  SD [auth 5],  SE [auth 5],  SF [auth 5],  SG [auth 5],  SH [auth 5],  TC [auth 5],  TD [auth 5],  TE [auth 5],  TF [auth 5],  TG [auth 5],  TH [auth 5],  UC [auth 5],  UD [auth 5],  UE [auth 5],  UF [auth 5],  UG [auth 5],  UH [auth 5],  VC [auth 5],  VD [auth 5],  VE [auth 5],  VF [auth 5],  VG [auth 5],  VH [auth 5],  WC [auth 5],  WD [auth 5],  WE [auth 5],  WF [auth 5],  WG [auth 5],  WH [auth 5],  XC [auth 5],  XD [auth 5],  XE [auth 5],  XF [auth 5],  XG [auth 5],  XH [auth 5],  YC [auth 5],  YD [auth 5],  YE [auth 5],  YF [auth 5],  YG [auth 5],  YH [auth 5],  ZC [auth 5],  ZD [auth 5],  ZE [auth 5],  ZF [auth 5],  ZG [auth 5],  ZH [auth 7]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.10 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 FoundationGermanyGRK1721

    Revision History  (Full details and data files)

    • Version 1.0: 2019-07-10
      Type: Initial release