6HCF

Structure of the rabbit 80S ribosome stalled on globin mRNA at the stop codon


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 2.0 of the entry. See complete history


Literature

ZNF598 Is a Quality Control Sensor of Collided Ribosomes.

Juszkiewicz, S.Chandrasekaran, V.Lin, Z.Kraatz, S.Ramakrishnan, V.Hegde, R.S.

(2018) Mol Cell 72: 469-481.e7

  • DOI: 10.1016/j.molcel.2018.08.037
  • Primary Citation of Related Structures:  
    6HCJ, 6HCM, 6HCF, 6HCQ

  • PubMed Abstract: 
  • Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates stalled ribosomes selectively is unclear. Here, we find that the minimal unit engaged by ZNF598 is the collided di-ribosome, a molecular species that arises when a trailing ribosome encounters a slower leading ribosome ...

    Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates stalled ribosomes selectively is unclear. Here, we find that the minimal unit engaged by ZNF598 is the collided di-ribosome, a molecular species that arises when a trailing ribosome encounters a slower leading ribosome. The collided di-ribosome structure reveals an extensive 40S-40S interface in which the ubiquitination targets of ZNF598 reside. The paucity of 60S interactions allows for different ribosome rotation states, explaining why ZNF598 recognition is indifferent to how the leading ribosome has stalled. The use of ribosome collisions as a proxy for stalling allows the degree of tolerable slowdown to be tuned by the initiation rate on that mRNA; hence, the threshold for triggering quality control is substrate specific. These findings illustrate how higher-order ribosome architecture can be exploited by cellular factors to monitor translation status.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. Electronic address: rhegde@mrc-lmb.cam.ac.uk.



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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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uS3E [auth E1]243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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eS4F [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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Ribosomal protein S9 (Predicted)K [auth K1]194Oryctolagus cuniculusMutation(s): 0 
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uS15O [auth O1]151Oryctolagus 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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RACK1HA [auth h1]317Oryctolagus cuniculusMutation(s): 0 
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eRF1(AAQ)IA [auth j1]439Homo sapiensMutation(s): 0 
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ATP binding cassette subfamily E member 1JA [auth k1]599Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L8NA [auth A3]257Oryctolagus cuniculusMutation(s): 0 
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uL3OA [auth B3]403Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L6QA [auth E3]291Oryctolagus cuniculusMutation(s): 0 
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uL30RA [auth F3]247Oryctolagus cuniculusMutation(s): 0 
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uL6SA [auth H3]192Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L14UA [auth M3]218Oryctolagus cuniculusMutation(s): 0 
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uL22XA [auth P3]184Oryctolagus cuniculusMutation(s): 0 
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eL18YA [auth Q3]188Oryctolagus cuniculusMutation(s): 0 
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eL21BB [auth T3]160Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L27HB [auth Z3]136Oryctolagus cuniculusMutation(s): 0 
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eL29JB [auth b3]226Oryctolagus cuniculusMutation(s): 0 
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eL32MB [auth e3]135Oryctolagus cuniculusMutation(s): 0 
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eL33NB [auth f3]110Oryctolagus cuniculusMutation(s): 0 
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uL29PB [auth h3]123Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L36QB [auth i3]105Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L37RB [auth j3]97Oryctolagus cuniculusMutation(s): 0 
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eL38SB [auth k3]70Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
eL39TB [auth l3]51Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
eL40UB [auth m3]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
eL41VB [auth n3]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
eL42WB [auth o3]106Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
eL43XB [auth p3]92Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
eL28YB [auth r3]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
uL10ZB [auth s3]318Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L12AC [auth t3]165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L11DC [auth J3]178Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
eL8EC [auth G3]319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5FC [auth D3]297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L10GC [auth I3]214Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetailsImage
nascent chainHC [auth 1]22Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 87
MoleculeChainsSequence LengthOrganismDetailsImage
uL1IC [auth u3]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: 37
MoleculeChainsLengthOrganismImage
28S ribosomal RNAKA [auth 52]3634Oryctolagus cuniculus
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Entity ID: 38
MoleculeChainsLengthOrganismImage
5S ribosomal RNALA [auth 72]120Oryctolagus cuniculus
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Entity ID: 39
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAMA [auth 82]156Oryctolagus cuniculus
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Entity ID: 80
MoleculeChainsLengthOrganismImage
P-site tRNABC [auth 23]76Oryctolagus cuniculus
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Entity ID: 81
MoleculeChainsLengthOrganismImage
mRNACC [auth w3]23Oryctolagus cuniculus
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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NF [auth k1], OF [auth k1]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AO [auth g3], CO [auth j3], DO [auth m3], EO [auth o3], FO [auth p3], KF [auth b1], LF [auth e1], MF [auth g1]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AD [auth A1] , AE [auth A1] , AF [auth A1] , AG [auth 52] , AH [auth 52] , AI [auth 52] , AJ [auth 52] , AK [auth 52] , 
AD [auth A1],  AE [auth A1],  AF [auth A1],  AG [auth 52],  AH [auth 52],  AI [auth 52],  AJ [auth 52],  AK [auth 52],  AL [auth 52],  AM [auth 52],  AN [auth 52],  BD [auth A1],  BE [auth A1],  BF [auth A1],  BG [auth 52],  BH [auth 52],  BI [auth 52],  BJ [auth 52],  BK [auth 52],  BL [auth 52],  BM [auth 52],  BN [auth 52],  BO [auth g3],  CD [auth A1],  CE [auth A1],  CF [auth A1],  CG [auth 52],  CH [auth 52],  CI [auth 52],  CJ [auth 52],  CK [auth 52],  CL [auth 52],  CM [auth 52],  CN [auth 52],  DD [auth A1],  DE [auth A1],  DF [auth A1],  DG [auth 52],  DH [auth 52],  DI [auth 52],  DJ [auth 52],  DK [auth 52],  DL [auth 52],  DM [auth 52],  DN [auth 52],  ED [auth A1],  EE [auth A1],  EF [auth A1],  EG [auth 52],  EH [auth 52],  EI [auth 52],  EJ [auth 52],  EK [auth 52],  EL [auth 52],  EM [auth 52],  EN [auth 52],  FD [auth A1],  FE [auth A1],  FF [auth A1],  FG [auth 52],  FH [auth 52],  FI [auth 52],  FJ [auth 52],  FK [auth 52],  FL [auth 52],  FM [auth 52],  FN [auth 52],  GD [auth A1],  GE [auth A1],  GF [auth A1],  GG [auth 52],  GH [auth 52],  GI [auth 52],  GJ [auth 52],  GK [auth 52],  GL [auth 52],  GM [auth 52],  GN [auth 52],  GO [auth w3],  HD [auth A1],  HE [auth A1],  HF [auth A1],  HG [auth 52],  HH [auth 52],  HI [auth 52],  HJ [auth 52],  HK [auth 52],  HL [auth 52],  HM [auth 52],  HN [auth 52],  ID [auth A1],  IE [auth A1],  IF [auth G1],  IG [auth 52],  IH [auth 52],  II [auth 52],  IJ [auth 52],  IK [auth 52],  IL [auth 52],  IM [auth 52],  IN [auth 52],  JC [auth A1],  JD [auth A1],  JE [auth A1],  JF [auth M1],  JG [auth 52],  JH [auth 52],  JI [auth 52],  JJ [auth 52],  JK [auth 52],  JL [auth 52],  JM [auth 52],  JN [auth 52],  KC [auth A1],  KD [auth A1],  KE [auth A1],  KG [auth 52],  KH [auth 52],  KI [auth 52],  KJ [auth 52],  KK [auth 52],  KL [auth 52],  KM [auth 52],  KN [auth 52],  LC [auth A1],  LD [auth A1],  LE [auth A1],  LG [auth 52],  LH [auth 52],  LI [auth 52],  LJ [auth 52],  LK [auth 52],  LL [auth 52],  LM [auth 52],  LN [auth 72],  MC [auth A1],  MD [auth A1],  ME [auth A1],  MG [auth 52],  MH [auth 52],  MI [auth 52],  MJ [auth 52],  MK [auth 52],  ML [auth 52],  MM [auth 52],  MN [auth 72],  NC [auth A1],  ND [auth A1],  NE [auth A1],  NG [auth 52],  NH [auth 52],  NI [auth 52],  NJ [auth 52],  NK [auth 52],  NL [auth 52],  NM [auth 52],  NN [auth 72],  OC [auth A1],  OD [auth A1],  OE [auth A1],  OG [auth 52],  OH [auth 52],  OI [auth 52],  OJ [auth 52],  OK [auth 52],  OL [auth 52],  OM [auth 52],  ON [auth 72],  PC [auth A1],  PD [auth A1],  PE [auth A1],  PF [auth 52],  PG [auth 52],  PH [auth 52],  PI [auth 52],  PJ [auth 52],  PK [auth 52],  PL [auth 52],  PM [auth 52],  PN [auth 72],  QC [auth A1],  QD [auth A1],  QE [auth A1],  QF [auth 52],  QG [auth 52],  QH [auth 52],  QI [auth 52],  QJ [auth 52],  QK [auth 52],  QL [auth 52],  QM [auth 52],  QN [auth 72],  RC [auth A1],  RD [auth A1],  RE [auth A1],  RF [auth 52],  RG [auth 52],  RH [auth 52],  RI [auth 52],  RJ [auth 52],  RK [auth 52],  RL [auth 52],  RM [auth 52],  RN [auth 72],  SC [auth A1],  SD [auth A1],  SE [auth A1],  SF [auth 52],  SG [auth 52],  SH [auth 52],  SI [auth 52],  SJ [auth 52],  SK [auth 52],  SL [auth 52],  SM [auth 52],  SN [auth 82],  TC [auth A1],  TD [auth A1],  TE [auth A1],  TF [auth 52],  TG [auth 52],  TH [auth 52],  TI [auth 52],  TJ [auth 52],  TK [auth 52],  TL [auth 52],  TM [auth 52],  TN [auth 82],  UC [auth A1],  UD [auth A1],  UE [auth A1],  UF [auth 52],  UG [auth 52],  UH [auth 52],  UI [auth 52],  UJ [auth 52],  UK [auth 52],  UL [auth 52],  UM [auth 52],  UN [auth 82],  VC [auth A1],  VD [auth A1],  VE [auth A1],  VF [auth 52],  VG [auth 52],  VH [auth 52],  VI [auth 52],  VJ [auth 52],  VK [auth 52],  VL [auth 52],  VM [auth 52],  VN [auth 82],  WC [auth A1],  WD [auth A1],  WE [auth A1],  WF [auth 52],  WG [auth 52],  WH [auth 52],  WI [auth 52],  WJ [auth 52],  WK [auth 52],  WL [auth 52],  WM [auth 52],  WN [auth 82],  XC [auth A1],  XD [auth A1],  XE [auth A1],  XF [auth 52],  XG [auth 52],  XH [auth 52],  XI [auth 52],  XJ [auth 52],  XK [auth 52],  XL [auth 52],  XM [auth 52],  XN [auth P3],  YC [auth A1],  YD [auth A1],  YE [auth A1],  YF [auth 52],  YG [auth 52],  YH [auth 52],  YI [auth 52],  YJ [auth 52],  YK [auth 52],  YL [auth 52],  YM [auth 52],  YN [auth V3],  ZC [auth A1],  ZD [auth A1],  ZE [auth A1],  ZF [auth 52],  ZG [auth 52],  ZH [auth 52],  ZI [auth 52],  ZJ [auth 52],  ZK [auth 52],  ZL [auth 52],  ZM [auth 52],  ZN [auth a3]
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
Medical Research Council (United Kingdom)United KingdomMC_UP_A022_1007
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570
Louis-Jeantet FoundationFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 2.0: 2019-01-23
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation