6SGC

Rabbit 80S ribosome stalled on a poly(A) tail


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

Mechanism of ribosome stalling during translation of a poly(A) tail.

Chandrasekaran, V.Juszkiewicz, S.Choi, J.Puglisi, J.D.Brown, A.Shao, S.Ramakrishnan, V.Hegde, R.S.

(2019) Nat Struct Mol Biol 26: 1132-1140

  • DOI: 10.1038/s41594-019-0331-x
  • Primary Citation of Related Structures:  
    6SGC

  • PubMed Abstract: 
  • Faulty or damaged messenger RNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation and ribosome recycling. The most common mRNA defect in eukaryotes is probably inappropriate polyadenylation at near-cognate sites within the coding region ...

    Faulty or damaged messenger RNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation and ribosome recycling. The most common mRNA defect in eukaryotes is probably inappropriate polyadenylation at near-cognate sites within the coding region. How ribosomes stall selectively when they encounter poly(A) is unclear. Here, we use biochemical and structural approaches in mammalian systems to show that poly-lysine, encoded by poly(A), favors a peptidyl-transfer RNA conformation suboptimal for peptide bond formation. This conformation partially slows elongation, permitting poly(A) mRNA in the ribosome's decoding center to adopt a ribosomal RNA-stabilized single-stranded helix. The reconfigured decoding center clashes with incoming aminoacyl-tRNA, thereby precluding elongation. Thus, coincidence detection of poly-lysine in the exit tunnel and poly(A) in the decoding center allows ribosomes to detect aberrant mRNAs selectively, stall elongation and trigger downstream quality control pathways essential for cellular homeostasis.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK. rhegde@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 2
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uS2B [auth B1]295Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S3aC [auth C1]264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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uS5D [auth D1]293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
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uS5E [auth E1]243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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40S ribosomal protein S4F [auth F1]263Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S5G [auth G1]204Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S6H [auth H1]249Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S7I [auth I1]194Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S8J [auth J1]208Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S9 (Predicted)K [auth K1]194Oryctolagus cuniculusMutation(s): 0 
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S10_plectin domain-ontaining proteinL [auth L1]165Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S12N [auth N1]132Oryctolagus cuniculusMutation(s): 0 
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uS19Q [auth Q1]145Oryctolagus cuniculusMutation(s): 0 
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eS17S [auth S1]135Oryctolagus cuniculusMutation(s): 0 
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eS13T [auth T1]152Oryctolagus cuniculusMutation(s): 0 
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Ribosomal_S10 domain-containing proteinV [auth V1]119Oryctolagus cuniculusMutation(s): 0 
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eS21W [auth W1]83Oryctolagus cuniculusMutation(s): 0 
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uS12Y [auth Y1]143Oryctolagus cuniculusMutation(s): 0 
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eS25AA [auth a1]125Oryctolagus cuniculusMutation(s): 0 
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eS26BA [auth b1]115Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S27CA [auth c1]84Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S28DA [auth d1]69Oryctolagus cuniculusMutation(s): 0 
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uS14EA [auth e1]56Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S30FA [auth f1]133Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S27aGA [auth g1]156Oryctolagus cuniculusMutation(s): 0 
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WD_REPEATS_REGION domain-containing proteinHA [auth h1]317Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L8JA [auth A2]257Oryctolagus cuniculusMutation(s): 0 
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uL3KA [auth B2]403Oryctolagus cuniculusMutation(s): 0 
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uL4LA [auth C2]425Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L5MA [auth D2]297Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L6NA [auth E2]291Oryctolagus cuniculusMutation(s): 0 
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uL30OA [auth F2]247Oryctolagus cuniculusMutation(s): 0 
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eL8PA [auth G2]319Oryctolagus cuniculusMutation(s): 0 
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uL6QA [auth H2]192Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L10RA [auth I2]214Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L11SA [auth J2]178Oryctolagus cuniculusMutation(s): 0 
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eL13TA [auth L2]211Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L14UA [auth M2]218Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L15VA [auth N2]204Oryctolagus cuniculusMutation(s): 0 
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uL13WA [auth O2]203Oryctolagus cuniculusMutation(s): 0 
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uL22XA [auth P2]184Oryctolagus cuniculusMutation(s): 0 
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eL18YA [auth Q2]188Oryctolagus cuniculusMutation(s): 0 
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eL19ZA [auth R2]196Oryctolagus cuniculusMutation(s): 0 
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eL20AB [auth S2]176Oryctolagus cuniculusMutation(s): 0 
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eL21BB [auth T2]160Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L23DB [auth V2]140Oryctolagus cuniculusMutation(s): 0 
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TRASH domain-containing proteinEB [auth W2]157Oryctolagus cuniculusMutation(s): 0 
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Ribosomal_L23eN domain-containing proteinFB [auth X2]156Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L26GB [auth Y2]145Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L27HB [auth Z2]136Oryctolagus cuniculusMutation(s): 0 
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Ribosomal_L18e/L15P domain-containing proteinIB [auth a2]148Oryctolagus cuniculusMutation(s): 0 
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eL29JB [auth b2]245Oryctolagus cuniculusMutation(s): 0 
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Ribosomal_L7Ae domain-containing proteinKB [auth c2]115Oryctolagus cuniculusMutation(s): 0 
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eL31LB [auth d2]125Oryctolagus cuniculusMutation(s): 0 
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eL32MB [auth e2]135Oryctolagus cuniculusMutation(s): 0 
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eL33NB [auth f2]110Oryctolagus cuniculusMutation(s): 0 
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eL34OB [auth g2]116Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
uL29PB [auth h2]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36QB [auth i2]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L37RB [auth j2]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
eL38SB [auth k2]70Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U001 (Oryctolagus cuniculus)
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Entity ID: 72
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eL39TB [auth l2]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
eL40UB [auth m2]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
60s ribosomal protein l41VB [auth n2]25Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
eL42WB [auth o2]106Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U344 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
eL43XB [auth p2]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal_L28e domain-containing proteinYB [auth r2]137Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
uL10ZB [auth s2]318Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L12AC [auth t2]165Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
poly-lysine nascent chainEC [auth XX]16Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal proteinFC [auth B]217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA [auth A1]1869Oryctolagus cuniculus
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  • Entity ID: 35
    MoleculeChainsLengthOrganismImage
    polyA mRNAIA [auth i1]10Homo sapiens
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    Entity ID: 80
    MoleculeChainsLengthOrganismImage
    28S ribosomal RNABC [auth 54]3603Oryctolagus cuniculus
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    Entity ID: 81
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNACC [auth 74]120Oryctolagus cuniculus
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    Entity ID: 82
    MoleculeChainsLengthOrganismImage
    5.8S ribosomal RNADC [auth 84]156Oryctolagus cuniculus
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    Entity ID: 85
    MoleculeChainsLengthOrganismImage
    tRNA (Lys3)GC [auth 23], HC [auth 33]76Oryctolagus cuniculus
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    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SPD
    Query on SPD

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    UM [auth 54], VM [auth 54]SPERMIDINE
    C7 H19 N3
    ATHGHQPFGPMSJY-UHFFFAOYSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    AF [auth b1], BF [auth e1], CF [auth g1], MF [auth g2], OF [auth j2], RF [auth m2], SF [auth o2], TF [auth p2]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AD [auth A1] , AE [auth A1] , AG [auth 54] , AH [auth 54] , AI [auth 54] , AJ [auth 54] , AK [auth 54] , AL [auth 54] , 
    AD [auth A1],  AE [auth A1],  AG [auth 54],  AH [auth 54],  AI [auth 54],  AJ [auth 54],  AK [auth 54],  AL [auth 54],  AM [auth 54],  AN [auth 74],  BD [auth A1],  BE [auth A1],  BG [auth 54],  BH [auth 54],  BI [auth 54],  BJ [auth 54],  BK [auth 54],  BL [auth 54],  BM [auth 54],  BN [auth 74],  CD [auth A1],  CE [auth A1],  CG [auth 54],  CH [auth 54],  CI [auth 54],  CJ [auth 54],  CK [auth 54],  CL [auth 54],  CM [auth 54],  CN [auth 84],  DD [auth A1],  DE [auth A1],  DF [auth A2],  DG [auth 54],  DH [auth 54],  DI [auth 54],  DJ [auth 54],  DK [auth 54],  DL [auth 54],  DM [auth 54],  DN [auth 84],  ED [auth A1],  EE [auth A1],  EF [auth B2],  EG [auth 54],  EH [auth 54],  EI [auth 54],  EJ [auth 54],  EK [auth 54],  EL [auth 54],  EM [auth 54],  EN [auth 84],  FD [auth A1],  FE [auth A1],  FF [auth I2],  FG [auth 54],  FH [auth 54],  FI [auth 54],  FJ [auth 54],  FK [auth 54],  FL [auth 54],  FM [auth 54],  FN [auth 84],  GD [auth A1],  GE [auth A1],  GF [auth P2],  GG [auth 54],  GH [auth 54],  GI [auth 54],  GJ [auth 54],  GK [auth 54],  GL [auth 54],  GM [auth 54],  GN [auth 84],  HD [auth A1],  HE [auth A1],  HF [auth Q2],  HG [auth 54],  HH [auth 54],  HI [auth 54],  HJ [auth 54],  HK [auth 54],  HL [auth 54],  HM [auth 54],  IC [auth A1],  ID [auth A1],  IE [auth A1],  IF [auth V2],  IG [auth 54],  IH [auth 54],  II [auth 54],  IJ [auth 54],  IK [auth 54],  IL [auth 54],  IM [auth 54],  JC [auth A1],  JD [auth A1],  JE [auth A1],  JF [auth a2],  JG [auth 54],  JH [auth 54],  JI [auth 54],  JJ [auth 54],  JK [auth 54],  JL [auth 54],  JM [auth 54],  KC [auth A1],  KD [auth A1],  KE [auth A1],  KF [auth a2],  KG [auth 54],  KH [auth 54],  KI [auth 54],  KJ [auth 54],  KK [auth 54],  KL [auth 54],  KM [auth 54],  LC [auth A1],  LD [auth A1],  LE [auth A1],  LF [auth e2],  LG [auth 54],  LH [auth 54],  LI [auth 54],  LJ [auth 54],  LK [auth 54],  LL [auth 54],  LM [auth 54],  MC [auth A1],  MD [auth A1],  ME [auth A1],  MG [auth 54],  MH [auth 54],  MI [auth 54],  MJ [auth 54],  MK [auth 54],  ML [auth 54],  MM [auth 54],  NC [auth A1],  ND [auth A1],  NE [auth A1],  NF [auth g2],  NG [auth 54],  NH [auth 54],  NI [auth 54],  NJ [auth 54],  NK [auth 54],  NL [auth 54],  NM [auth 54],  OC [auth A1],  OD [auth A1],  OE [auth A1],  OG [auth 54],  OH [auth 54],  OI [auth 54],  OJ [auth 54],  OK [auth 54],  OL [auth 54],  OM [auth 54],  PC [auth A1],  PD [auth A1],  PE [auth A1],  PF [auth j2],  PG [auth 54],  PH [auth 54],  PI [auth 54],  PJ [auth 54],  PK [auth 54],  PL [auth 54],  PM [auth 54],  QC [auth A1],  QD [auth A1],  QE [auth A1],  QF [auth j2],  QG [auth 54],  QH [auth 54],  QI [auth 54],  QJ [auth 54],  QK [auth 54],  QL [auth 54],  QM [auth 54],  RC [auth A1],  RD [auth A1],  RE [auth A1],  RG [auth 54],  RH [auth 54],  RI [auth 54],  RJ [auth 54],  RK [auth 54],  RL [auth 54],  RM [auth 54],  SC [auth A1],  SD [auth A1],  SE [auth A1],  SG [auth 54],  SH [auth 54],  SI [auth 54],  SJ [auth 54],  SK [auth 54],  SL [auth 54],  SM [auth 54],  TC [auth A1],  TD [auth A1],  TE [auth A1],  TG [auth 54],  TH [auth 54],  TI [auth 54],  TJ [auth 54],  TK [auth 54],  TL [auth 54],  TM [auth 54],  UC [auth A1],  UD [auth A1],  UE [auth A1],  UF [auth 54],  UG [auth 54],  UH [auth 54],  UI [auth 54],  UJ [auth 54],  UK [auth 54],  UL [auth 54],  VC [auth A1],  VD [auth A1],  VE [auth A1],  VF [auth 54],  VG [auth 54],  VH [auth 54],  VI [auth 54],  VJ [auth 54],  VK [auth 54],  VL [auth 54],  WC [auth A1],  WD [auth A1],  WE [auth A1],  WF [auth 54],  WG [auth 54],  WH [auth 54],  WI [auth 54],  WJ [auth 54],  WK [auth 54],  WL [auth 54],  WM [auth 74],  XC [auth A1],  XD [auth A1],  XE [auth A1],  XF [auth 54],  XG [auth 54],  XH [auth 54],  XI [auth 54],  XJ [auth 54],  XK [auth 54],  XL [auth 54],  XM [auth 74],  YC [auth A1],  YD [auth A1],  YE [auth A1],  YF [auth 54],  YG [auth 54],  YH [auth 54],  YI [auth 54],  YJ [auth 54],  YK [auth 54],  YL [auth 54],  YM [auth 74],  ZC [auth A1],  ZD [auth A1],  ZE [auth A1],  ZF [auth 54],  ZG [auth 54],  ZH [auth 54],  ZI [auth 54],  ZJ [auth 54],  ZK [auth 54],  ZL [auth 54],  ZM [auth 74]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 2.80 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Medical Research Council (United Kingdom)United KingdomMC_UP_A022_1007
    Medical Research Council (United Kingdom)United KingdomMC_U105184332
    Wellcome TrustUnited KingdomWT096570
    National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM51266
    National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM113078

    Revision History  (Full details and data files)

    • Version 1.0: 2019-12-04
      Type: Initial release
    • Version 1.1: 2019-12-18
      Changes: Database references