6R7Q

Structure of XBP1u-paused ribosome nascent chain complex with Sec61.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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: 1
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40S ribosomal protein S30A [auth AA]55Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S7B [auth BB]189Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S8C [auth CC]206Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S9 (Predicted)D [auth DD]185Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S11E [auth EE]151Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S28F [auth FF]62Oryctolagus cuniculusMutation(s): 0 
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uS10G [auth GG]100Oryctolagus cuniculusMutation(s): 0 
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eS21H [auth HH]83Oryctolagus cuniculusMutation(s): 0 
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uS13I [auth II]144Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S27J [auth JJ]83Oryctolagus cuniculusMutation(s): 0 
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eS17K [auth KK]132Oryctolagus cuniculusMutation(s): 0 
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eS26L [auth LL]101Oryctolagus cuniculusMutation(s): 0 
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uS11M [auth MM]136Oryctolagus cuniculusMutation(s): 0 
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eS31N [auth 0]68Oryctolagus cuniculusMutation(s): 0 
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X-box-binding protein 1O [auth 1]24Homo sapiensMutation(s): 0 
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ribosomal protein RACK1T [auth 6]313Oryctolagus cuniculusMutation(s): 0 
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uS14W [auth 9]55Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS25Y [auth OO]75Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS15AA [auth QQ]149Oryctolagus cuniculusMutation(s): 0 
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uL2CA [auth A]248Oryctolagus cuniculusMutation(s): 0 
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uL3DA [auth B]394Oryctolagus cuniculusMutation(s): 0 
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uL4EA [auth C]362Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L5FA [auth D]293Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L6GA [auth E]251Oryctolagus cuniculusMutation(s): 0 
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uL30HA [auth F]225Oryctolagus cuniculusMutation(s): 0 
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eL8IA [auth G]240Oryctolagus cuniculusMutation(s): 0 
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uL6JA [auth H]190Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L10 (Predicted)KA [auth I]213Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L11LA [auth J]170Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L13NA [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L14OA [auth M]138Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L15PA [auth N]203Oryctolagus cuniculusMutation(s): 0 
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uL13QA [auth O]199Oryctolagus cuniculusMutation(s): 0 
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uL22RA [auth P]153Oryctolagus cuniculusMutation(s): 0 
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eL18SA [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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eL19TA [auth R]180Oryctolagus cuniculusMutation(s): 0 
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eL20UA [auth S]176Oryctolagus cuniculusMutation(s): 0 
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eL21VA [auth T]159Oryctolagus cuniculusMutation(s): 0 
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eL14XA [auth V]131Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L24YA [auth W]121Oryctolagus cuniculusMutation(s): 0 
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uL23ZA [auth X]118Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L26AB [auth Y]134Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L27BB [auth Z]135Oryctolagus cuniculusMutation(s): 0 
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eS10CB [auth SS]96Oryctolagus cuniculusMutation(s): 0 
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uL15DB [auth a]147Oryctolagus cuniculusMutation(s): 0 
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eL29EB [auth b]116Oryctolagus cuniculusMutation(s): 0 
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eL30FB [auth c]98Oryctolagus cuniculusMutation(s): 0 
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eL31GB [auth d]107Oryctolagus cuniculusMutation(s): 0 
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eL32HB [auth e]128Oryctolagus cuniculusMutation(s): 0 
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eL33IB [auth f]109Oryctolagus cuniculusMutation(s): 0 
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eL34JB [auth g]114Oryctolagus cuniculusMutation(s): 0 
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uL29KB [auth h]122Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L36LB [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L37MB [auth j]86Oryctolagus cuniculusMutation(s): 0 
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eL38NB [auth k]69Oryctolagus cuniculusMutation(s): 0 
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eL39OB [auth l]50Oryctolagus cuniculusMutation(s): 0 
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eL40PB [auth m]52Oryctolagus cuniculusMutation(s): 0 
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60s ribosomal protein l41QB [auth n]25Oryctolagus cuniculusMutation(s): 0 
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eL42RB [auth o]104Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL43SB [auth p]91Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
uS2TB [auth q]217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
eL28UB [auth r]124Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 74
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60S acidic ribosomal protein P0VB [auth s]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
uL11WB [auth t]153Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 76
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40S ribosomal protein S3aXB [auth u]213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
uS5YB [auth v]221Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
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Ribosomal protein S3ZB [auth w]228Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4AC [auth x]262Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 80
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Ribosomal protein S5BC [auth y]191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
Find proteins for G1TFM5 (Oryctolagus cuniculus)
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Entity ID: 81
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40S ribosomal protein S6CC [auth z]237Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S15aDC [auth TT]129Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 83
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Ribosomal protein S16EC [auth UU]142Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SGX4 (Oryctolagus cuniculus)
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Entity ID: 84
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Ribosomal protein S23FC [auth VV]141Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 85
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uS19GC [auth WW]120Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 86
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Protein transport protein Sec61 subunit alpha isoform 1HC [auth XX]461Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61A1
Find proteins for P38377 (Canis lupus familiaris)
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Entity ID: 87
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit gammaIC [auth YY]62Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61G
Find proteins for P60058 (Canis lupus familiaris)
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Entity ID: 88
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit betaJC [auth ZZ]29Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61B
Find proteins for P60467 (Canis lupus familiaris)
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Entity ID: 16
MoleculeChainsLengthOrganismImage
P-tRNAP [auth 2]75Saccharomyces cerevisiae
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Entity ID: 17
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E-tRNAQ [auth 3]75Saccharomyces cerevisiae
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  • Entity ID: 18
    MoleculeChainsLengthOrganismImage
    messenger RNAR [auth 4]6Homo sapiens
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    Entity ID: 19
    MoleculeChainsLengthOrganismImage
    28S ribosomal RNAS [auth 5]3544Oryctolagus cuniculus
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    Entity ID: 21
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNAU [auth 7]120Oryctolagus cuniculus
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    Entity ID: 22
    MoleculeChainsLengthOrganismImage
    5.8S ribosomal RNAV [auth 8]151Oryctolagus cuniculus
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    Entity ID: 39
    MoleculeChainsLengthOrganismImage
    18S ribosomal RNAMA [auth K]1698Oryctolagus cuniculus
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    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    AO [auth o], BO [auth p], KC [auth LL], VN [auth g], XN [auth j], ZN [auth m]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 5] , AJ [auth 5] , AK [auth 5] , 
    AD [auth 5],  AE [auth 5],  AF [auth 5],  AG [auth 5],  AH [auth 5],  AI [auth 5],  AJ [auth 5],  AK [auth 5],  AL [auth K],  AM [auth K],  AN [auth K],  BD [auth 5],  BE [auth 5],  BF [auth 5],  BG [auth 5],  BH [auth 5],  BI [auth 5],  BJ [auth 5],  BK [auth 5],  BL [auth K],  BM [auth K],  BN [auth K],  CD [auth 5],  CE [auth 5],  CF [auth 5],  CG [auth 5],  CH [auth 5],  CI [auth 5],  CJ [auth 5],  CK [auth 5],  CL [auth K],  CM [auth K],  CN [auth K],  CO [auth y],  DD [auth 5],  DE [auth 5],  DF [auth 5],  DG [auth 5],  DH [auth 5],  DI [auth 5],  DJ [auth 5],  DK [auth 5],  DL [auth K],  DM [auth K],  DN [auth K],  ED [auth 5],  EE [auth 5],  EF [auth 5],  EG [auth 5],  EH [auth 5],  EI [auth 5],  EJ [auth 5],  EK [auth 7],  EL [auth K],  EM [auth K],  EN [auth K],  FD [auth 5],  FE [auth 5],  FF [auth 5],  FG [auth 5],  FH [auth 5],  FI [auth 5],  FJ [auth 5],  FK [auth 7],  FL [auth K],  FM [auth K],  FN [auth K],  GD [auth 5],  GE [auth 5],  GF [auth 5],  GG [auth 5],  GH [auth 5],  GI [auth 5],  GJ [auth 5],  GK [auth 7],  GL [auth K],  GM [auth K],  GN [auth K],  HD [auth 5],  HE [auth 5],  HF [auth 5],  HG [auth 5],  HH [auth 5],  HI [auth 5],  HJ [auth 5],  HK [auth 7],  HL [auth K],  HM [auth K],  HN [auth K],  ID [auth 5],  IE [auth 5],  IF [auth 5],  IG [auth 5],  IH [auth 5],  II [auth 5],  IJ [auth 5],  IK [auth 7],  IL [auth K],  IM [auth K],  IN [auth K],  JD [auth 5],  JE [auth 5],  JF [auth 5],  JG [auth 5],  JH [auth 5],  JI [auth 5],  JJ [auth 5],  JK [auth 7],  JL [auth K],  JM [auth K],  JN [auth K],  KD [auth 5],  KE [auth 5],  KF [auth 5],  KG [auth 5],  KH [auth 5],  KI [auth 5],  KJ [auth 5],  KK [auth 7],  KL [auth K],  KM [auth K],  KN [auth K],  LC [auth 5],  LD [auth 5],  LE [auth 5],  LF [auth 5],  LG [auth 5],  LH [auth 5],  LI [auth 5],  LJ [auth 5],  LK [auth 8],  LL [auth K],  LM [auth K],  LN [auth K],  MC [auth 5],  MD [auth 5],  ME [auth 5],  MF [auth 5],  MG [auth 5],  MH [auth 5],  MI [auth 5],  MJ [auth 5],  MK [auth 8],  ML [auth K],  MM [auth K],  MN [auth K],  NC [auth 5],  ND [auth 5],  NE [auth 5],  NF [auth 5],  NG [auth 5],  NH [auth 5],  NI [auth 5],  NJ [auth 5],  NK [auth 8],  NL [auth K],  NM [auth K],  NN [auth K],  OC [auth 5],  OD [auth 5],  OE [auth 5],  OF [auth 5],  OG [auth 5],  OH [auth 5],  OI [auth 5],  OJ [auth 5],  OK [auth 8],  OL [auth K],  OM [auth K],  ON [auth K],  PC [auth 5],  PD [auth 5],  PE [auth 5],  PF [auth 5],  PG [auth 5],  PH [auth 5],  PI [auth 5],  PJ [auth 5],  PK [auth B],  PL [auth K],  PM [auth K],  PN [auth K],  QC [auth 5],  QD [auth 5],  QE [auth 5],  QF [auth 5],  QG [auth 5],  QH [auth 5],  QI [auth 5],  QJ [auth 5],  QK [auth K],  QL [auth K],  QM [auth K],  QN [auth P],  RC [auth 5],  RD [auth 5],  RE [auth 5],  RF [auth 5],  RG [auth 5],  RH [auth 5],  RI [auth 5],  RJ [auth 5],  RK [auth K],  RL [auth K],  RM [auth K],  RN [auth P],  SC [auth 5],  SD [auth 5],  SE [auth 5],  SF [auth 5],  SG [auth 5],  SH [auth 5],  SI [auth 5],  SJ [auth 5],  SK [auth K],  SL [auth K],  SM [auth K],  SN [auth V],  TC [auth 5],  TD [auth 5],  TE [auth 5],  TF [auth 5],  TG [auth 5],  TH [auth 5],  TI [auth 5],  TJ [auth 5],  TK [auth K],  TL [auth K],  TM [auth K],  TN [auth a],  UC [auth 5],  UD [auth 5],  UE [auth 5],  UF [auth 5],  UG [auth 5],  UH [auth 5],  UI [auth 5],  UJ [auth 5],  UK [auth K],  UL [auth K],  UM [auth K],  UN [auth e],  VC [auth 5],  VD [auth 5],  VE [auth 5],  VF [auth 5],  VG [auth 5],  VH [auth 5],  VI [auth 5],  VJ [auth 5],  VK [auth K],  VL [auth K],  VM [auth K],  WC [auth 5],  WD [auth 5],  WE [auth 5],  WF [auth 5],  WG [auth 5],  WH [auth 5],  WI [auth 5],  WJ [auth 5],  WK [auth K],  WL [auth K],  WM [auth K],  WN [auth g],  XC [auth 5],  XD [auth 5],  XE [auth 5],  XF [auth 5],  XG [auth 5],  XH [auth 5],  XI [auth 5],  XJ [auth 5],  XK [auth K],  XL [auth K],  XM [auth K],  YC [auth 5],  YD [auth 5],  YE [auth 5],  YF [auth 5],  YG [auth 5],  YH [auth 5],  YI [auth 5],  YJ [auth 5],  YK [auth K],  YL [auth K],  YM [auth K],  YN [auth j],  ZC [auth 5],  ZD [auth 5],  ZE [auth 5],  ZF [auth 5],  ZG [auth 5],  ZH [auth 5],  ZI [auth 5],  ZJ [auth 5],  ZK [auth K],  ZL [auth K],  ZM [auth K]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 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 FoundationGermany--

    Revision History  (Full details and data files)

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