6T4Q

Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts.

Tesina, P.Lessen, L.N.Buschauer, R.Cheng, J.Wu, C.C.Berninghausen, O.Buskirk, A.R.Becker, T.Beckmann, R.Green, R.

(2020) EMBO J 39: e103365-e103365

  • DOI: 10.15252/embj.2019103365
  • Primary Citation of Related Structures:  
    6T4Q, 6T83, 6T7T, 6T7I

  • PubMed Abstract: 
  • Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mechanisms that lead to these ribosome stalls ...

    Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mechanisms that lead to these ribosome stalls. First, we use an in vitro reconstituted yeast translation system to demonstrate that inhibitory codon pairs slow elongation rates which are partially rescued by increased tRNA concentration or by an artificial tRNA not dependent on wobble base-pairing. Ribosome profiling data extend these observations by revealing that paused ribosomes with empty A sites are enriched on these sequences. Cryo-EM structures of stalled ribosomes provide a structural explanation for the observed effects by showing decoding-incompatible conformations of mRNA in the A sites of all studied stall- and collision-inducing sequences. Interestingly, in the case of poly(A) tracts, the inhibitory conformation of the mRNA in the A site involves a nucleotide stacking array. Together, these data demonstrate a novel mRNA-induced mechanisms of translational stalling in eukaryotic ribosomes.


    Organizational Affiliation

    Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.



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40S ribosomal protein S1-AB [auth SB]232Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15C [auth SP]117Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2D [auth SC]216Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3E [auth SD]222Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-AF [auth SE]258Saccharomyces cerevisiaeMutation(s): 0 
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Rps5pG [auth SF]206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-AH [auth SG]228Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-AI [auth SH]184Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-AJ [auth SI]198Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-AK [auth SJ]184Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-AL [auth SK]92Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-AM [auth SL]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12N [auth SM]121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13O [auth SN]150Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-BP [auth SO]127Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-AQ [auth SQ]141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-AR [auth SR]125Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-AS [auth SS]145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-AT [auth ST]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20U [auth SU]100Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S21-AV [auth SV]87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22-AW [auth SW]129Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-AX [auth SX]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-AY [auth SY]134Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-AZ [auth SZ]82Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S26-BAA [auth Sa]97Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-ABA [auth Sb]81Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-ACA [auth Sd]53Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S30-ADA [auth Se]60Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31EA [auth Sf]73Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like proteinFA [auth Sg]312Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-AGA [auth Sc]63Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-AJA [auth LA]251Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3KA [auth LB]386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-ALA [auth LC]361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5MA [auth LD]294Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-BNA [auth LE]175Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-AOA [auth LF]222Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-APA [auth LG]233Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-AQA [auth LH]191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10RA [auth LI]218Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-BSA [auth LJ]169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-ATA [auth LL]193Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AUA [auth LM]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-AVA [auth LN]203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AWA [auth LO]197Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AXA [auth LP]183Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-AYA [auth LQ]185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-AZA [auth LR]188Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-AAB [auth LS]171Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-ABB [auth LT]159Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-ACB [auth LU]100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-ADB [auth LV]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-AEB [auth LW]126Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25FB [auth LX]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-AGB [auth LY]125Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-AHB [auth LZ]135Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28IB [auth La]148Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29JB [auth Lb]58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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60S ribosomal protein L30KB [auth Lc]96Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-ALB [auth Ld]109Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32MB [auth Le]127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33-ANB [auth Lf]106Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L34-AOB [auth Lg]112Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35-APB [auth Lh]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S ribosomal protein L36-AQB [auth Li]99Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37-ARB [auth Lj]85Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L38SB [auth Lk]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S ribosomal protein L39TB [auth Ll]50Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-60S ribosomal protein L40UB [auth Lm]52Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L41-AVB [auth Ln]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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60S ribosomal protein L42-AWB [auth Lo]103Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43-AXB [auth Lp]91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 81
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nascent chainCC [auth 8]6Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 82
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40S ribosomal protein S0-ADC [auth SA]206Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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18S rRNAA [auth C2]1798Saccharomyces cerevisiae
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Entity ID: 34
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5S rRNAHA [auth C4]121Saccharomyces cerevisiae
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Entity ID: 35
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5.8S rRNAIA [auth C3]158Saccharomyces cerevisiae
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Entity ID: 77
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25S rRNAYB [auth C1]3184Saccharomyces cerevisiae
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Entity ID: 78
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mRNAZB [auth 5]30Saccharomyces cerevisiae
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Entity ID: 79
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ICG tRNA Arg (P/P)AC [auth 6]76Saccharomyces cerevisiae
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Entity ID: 80
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tRNA (E/E)BC [auth 7]75Saccharomyces cerevisiae
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
EG [auth Lg], FG [auth Lj], HG [auth Lm], IG [auth Lo], JG [auth Lp], LF [auth Sd], MF [auth Sf]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AD [auth C2] , AE [auth C2] , AF [auth C2] , AG [auth La] , AH [auth C1] , AI [auth C1] , AJ [auth C1] , AK [auth C1] , 
AD [auth C2],  AE [auth C2],  AF [auth C2],  AG [auth La],  AH [auth C1],  AI [auth C1],  AJ [auth C1],  AK [auth C1],  AL [auth C1],  AM [auth C1],  AN [auth C1],  BD [auth C2],  BE [auth C2],  BF [auth C2],  BG [auth Le],  BH [auth C1],  BI [auth C1],  BJ [auth C1],  BK [auth C1],  BL [auth C1],  BM [auth C1],  BN [auth C1],  CD [auth C2],  CE [auth C2],  CF [auth C2],  CG [auth Le],  CH [auth C1],  CI [auth C1],  CJ [auth C1],  CK [auth C1],  CL [auth C1],  CM [auth C1],  CN [auth C1],  DD [auth C2],  DE [auth C2],  DF [auth C2],  DG [auth Lg],  DH [auth C1],  DI [auth C1],  DJ [auth C1],  DK [auth C1],  DL [auth C1],  DM [auth C1],  DN [auth C1],  EC [auth C2],  ED [auth C2],  EE [auth C2],  EF [auth C2],  EH [auth C1],  EI [auth C1],  EJ [auth C1],  EK [auth C1],  EL [auth C1],  EM [auth C1],  EN [auth C1],  FC [auth C2],  FD [auth C2],  FE [auth C2],  FF [auth C2],  FH [auth C1],  FI [auth C1],  FJ [auth C1],  FK [auth C1],  FL [auth C1],  FM [auth C1],  FN [auth C1],  GC [auth C2],  GD [auth C2],  GE [auth C2],  GF [auth C2],  GG [auth Lj],  GH [auth C1],  GI [auth C1],  GJ [auth C1],  GK [auth C1],  GL [auth C1],  GM [auth C1],  GN [auth C1],  HC [auth C2],  HD [auth C2],  HE [auth C2],  HF [auth C2],  HH [auth C1],  HI [auth C1],  HJ [auth C1],  HK [auth C1],  HL [auth C1],  HM [auth C1],  HN [auth C1],  IC [auth C2],  ID [auth C2],  IE [auth C2],  IF [auth C2],  IH [auth C1],  II [auth C1],  IJ [auth C1],  IK [auth C1],  IL [auth C1],  IM [auth C1],  IN [auth C1],  JC [auth C2],  JD [auth C2],  JE [auth C2],  JF [auth C2],  JH [auth C1],  JI [auth C1],  JJ [auth C1],  JK [auth C1],  JL [auth C1],  JM [auth C1],  JN [auth C1],  KC [auth C2],  KD [auth C2],  KE [auth C2],  KF [auth SF],  KG [auth C1],  KH [auth C1],  KI [auth C1],  KJ [auth C1],  KK [auth C1],  KL [auth C1],  KM [auth C1],  KN [auth C1],  LC [auth C2],  LD [auth C2],  LE [auth C2],  LG [auth C1],  LH [auth C1],  LI [auth C1],  LJ [auth C1],  LK [auth C1],  LL [auth C1],  LM [auth C1],  LN [auth C1],  MC [auth C2],  MD [auth C2],  ME [auth C2],  MG [auth C1],  MH [auth C1],  MI [auth C1],  MJ [auth C1],  MK [auth C1],  ML [auth C1],  MM [auth C1],  MN [auth C1],  NC [auth C2],  ND [auth C2],  NE [auth C2],  NF [auth C4],  NG [auth C1],  NH [auth C1],  NI [auth C1],  NJ [auth C1],  NK [auth C1],  NL [auth C1],  NM [auth C1],  NN [auth C1],  OC [auth C2],  OD [auth C2],  OE [auth C2],  OF [auth C3],  OG [auth C1],  OH [auth C1],  OI [auth C1],  OJ [auth C1],  OK [auth C1],  OL [auth C1],  OM [auth C1],  ON [auth C1],  PC [auth C2],  PD [auth C2],  PE [auth C2],  PF [auth LA],  PG [auth C1],  PH [auth C1],  PI [auth C1],  PJ [auth C1],  PK [auth C1],  PL [auth C1],  PM [auth C1],  PN [auth 6],  QC [auth C2],  QD [auth C2],  QE [auth C2],  QF [auth LA],  QG [auth C1],  QH [auth C1],  QI [auth C1],  QJ [auth C1],  QK [auth C1],  QL [auth C1],  QM [auth C1],  RC [auth C2],  RD [auth C2],  RE [auth C2],  RF [auth LB],  RG [auth C1],  RH [auth C1],  RI [auth C1],  RJ [auth C1],  RK [auth C1],  RL [auth C1],  RM [auth C1],  SC [auth C2],  SD [auth C2],  SE [auth C2],  SF [auth LB],  SG [auth C1],  SH [auth C1],  SI [auth C1],  SJ [auth C1],  SK [auth C1],  SL [auth C1],  SM [auth C1],  TC [auth C2],  TD [auth C2],  TE [auth C2],  TF [auth LF],  TG [auth C1],  TH [auth C1],  TI [auth C1],  TJ [auth C1],  TK [auth C1],  TL [auth C1],  TM [auth C1],  UC [auth C2],  UD [auth C2],  UE [auth C2],  UF [auth LN],  UG [auth C1],  UH [auth C1],  UI [auth C1],  UJ [auth C1],  UK [auth C1],  UL [auth C1],  UM [auth C1],  VC [auth C2],  VD [auth C2],  VE [auth C2],  VF [auth LN],  VG [auth C1],  VH [auth C1],  VI [auth C1],  VJ [auth C1],  VK [auth C1],  VL [auth C1],  VM [auth C1],  WC [auth C2],  WD [auth C2],  WE [auth C2],  WF [auth LP],  WG [auth C1],  WH [auth C1],  WI [auth C1],  WJ [auth C1],  WK [auth C1],  WL [auth C1],  WM [auth C1],  XC [auth C2],  XD [auth C2],  XE [auth C2],  XF [auth LR],  XG [auth C1],  XH [auth C1],  XI [auth C1],  XJ [auth C1],  XK [auth C1],  XL [auth C1],  XM [auth C1],  YC [auth C2],  YD [auth C2],  YE [auth C2],  YF [auth LR],  YG [auth C1],  YH [auth C1],  YI [auth C1],  YJ [auth C1],  YK [auth C1],  YL [auth C1],  YM [auth C1],  ZC [auth C2],  ZD [auth C2],  ZE [auth C2],  ZF [auth LV],  ZG [auth C1],  ZH [auth C1],  ZI [auth C1],  ZJ [auth C1],  ZK [auth C1],  ZL [auth C1],  ZM [auth C1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 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 FoundationGermanyBE1814/15-1

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2020-02-12
    Changes: Database references