6HCQ

Structure of the rabbit collided di-ribosome (collided monosome)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 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

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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Entity ID: 5
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uS2E [auth B2]295Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S3aF [auth C2]264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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eS1G [auth D2]293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
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uS3H [auth E2]243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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eS4I [auth F2]263Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S5J [auth G2]204Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S6K [auth H2]249Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S7L [auth I2]194Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S9 (Predicted)N [auth K2]194Oryctolagus cuniculusMutation(s): 0 
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uS15R [auth O2]151Oryctolagus cuniculusMutation(s): 0 
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eS26EA [auth b2]115Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S27FA [auth c2]84Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S28GA [auth d2]69Oryctolagus cuniculusMutation(s): 0 
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uS14HA [auth e2]56Oryctolagus cuniculusMutation(s): 0 
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RACK1KA [auth h2]317Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L8LA [auth A3]257Oryctolagus cuniculusMutation(s): 0 
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uL3MA [auth B3]403Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L5OA [auth D3]297Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L6PA [auth E3]291Oryctolagus cuniculusMutation(s): 0 
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uL30QA [auth F3]247Oryctolagus cuniculusMutation(s): 0 
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eL8RA [auth G3]319Oryctolagus cuniculusMutation(s): 0 
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uL6SA [auth H3]192Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L10TA [auth I3]214Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L11UA [auth J3]178Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L14WA [auth M3]218Oryctolagus cuniculusMutation(s): 0 
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uL22ZA [auth P3]184Oryctolagus cuniculusMutation(s): 0 
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eL18AB [auth Q3]188Oryctolagus cuniculusMutation(s): 0 
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eL20CB [auth S3]176Oryctolagus cuniculusMutation(s): 0 
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eL21DB [auth T3]160Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L23FB [auth V3]140Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L26HB [auth Y3]145Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L27IB [auth Z3]136Oryctolagus cuniculusMutation(s): 0 
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uL15JB [auth a3]148Oryctolagus cuniculusMutation(s): 0 
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eL29KB [auth b3]245Oryctolagus cuniculusMutation(s): 0 
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eL30LB [auth c3]115Oryctolagus cuniculusMutation(s): 0 
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eL31MB [auth d3]125Oryctolagus cuniculusMutation(s): 0 
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eL32NB [auth e3]135Oryctolagus cuniculusMutation(s): 0 
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eL33OB [auth f3]110Oryctolagus cuniculusMutation(s): 0 
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eL34PB [auth g3]117Oryctolagus cuniculusMutation(s): 0 
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uL29QB [auth h3]123Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L36RB [auth i3]105Oryctolagus cuniculusMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L37SB [auth j3]97Oryctolagus cuniculusMutation(s): 0 
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
eL38TB [auth k3]70Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
eL39UB [auth l3]51Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
eL40VB [auth m3]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
eL41WB [auth n3]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
eL42XB [auth o3]106Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
eL43YB [auth p3]92Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
eL28ZB [auth r3]137Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
uL10BC [auth t3]318Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L12CC [auth u3]165Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal proteinFC [auth w3]217Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SKZ8 (Oryctolagus cuniculus)
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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetailsImage
nascent chainGC [auth 1]22Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
28S ribosomal RNAA [auth 51]3635Oryctolagus cuniculus
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth 71]120Oryctolagus cuniculus
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAC [auth 81]156Oryctolagus cuniculus
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Entity ID: 4
MoleculeChainsLengthOrganismImage
18S ribosomal RNAD [auth A2]1869Oryctolagus cuniculus
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Entity ID: 79
MoleculeChainsLengthOrganismImage
A/P tRNAAC [auth q3]74Oryctolagus cuniculus
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Entity ID: 82
MoleculeChainsLengthOrganismImage
mRNADC [auth v3]22Oryctolagus cuniculus
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Entity ID: 83
MoleculeChainsLengthOrganismImage
P/E tRNAEC [auth 33]75Oryctolagus 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 o3], BO [auth p3], LN [auth b2], MN [auth e2], ON [auth g2], XN [auth g3], YN [auth j3], ZN [auth m3]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AD [auth 51] , AE [auth 51] , AF [auth 51] , AG [auth 51] , AH [auth 51] , AI [auth 51] , AJ [auth 51] , AK [auth 71] , 
AD [auth 51],  AE [auth 51],  AF [auth 51],  AG [auth 51],  AH [auth 51],  AI [auth 51],  AJ [auth 51],  AK [auth 71],  AL [auth A2],  AM [auth A2],  AN [auth A2],  BD [auth 51],  BE [auth 51],  BF [auth 51],  BG [auth 51],  BH [auth 51],  BI [auth 51],  BJ [auth 51],  BK [auth 71],  BL [auth A2],  BM [auth A2],  BN [auth A2],  CD [auth 51],  CE [auth 51],  CF [auth 51],  CG [auth 51],  CH [auth 51],  CI [auth 51],  CJ [auth 51],  CK [auth 71],  CL [auth A2],  CM [auth A2],  CN [auth A2],  CO [auth q3],  DD [auth 51],  DE [auth 51],  DF [auth 51],  DG [auth 51],  DH [auth 51],  DI [auth 51],  DJ [auth 51],  DK [auth 71],  DL [auth A2],  DM [auth A2],  DN [auth A2],  ED [auth 51],  EE [auth 51],  EF [auth 51],  EG [auth 51],  EH [auth 51],  EI [auth 51],  EJ [auth 51],  EK [auth 71],  EL [auth A2],  EM [auth A2],  EN [auth A2],  FD [auth 51],  FE [auth 51],  FF [auth 51],  FG [auth 51],  FH [auth 51],  FI [auth 51],  FJ [auth 51],  FK [auth 81],  FL [auth A2],  FM [auth A2],  FN [auth A2],  GD [auth 51],  GE [auth 51],  GF [auth 51],  GG [auth 51],  GH [auth 51],  GI [auth 51],  GJ [auth 51],  GK [auth 81],  GL [auth A2],  GM [auth A2],  GN [auth A2],  HC [auth 51],  HD [auth 51],  HE [auth 51],  HF [auth 51],  HG [auth 51],  HH [auth 51],  HI [auth 51],  HJ [auth 51],  HK [auth 81],  HL [auth A2],  HM [auth A2],  HN [auth A2],  IC [auth 51],  ID [auth 51],  IE [auth 51],  IF [auth 51],  IG [auth 51],  IH [auth 51],  II [auth 51],  IJ [auth 51],  IK [auth 81],  IL [auth A2],  IM [auth A2],  IN [auth A2],  JC [auth 51],  JD [auth 51],  JE [auth 51],  JF [auth 51],  JG [auth 51],  JH [auth 51],  JI [auth 51],  JJ [auth 51],  JK [auth 81],  JL [auth A2],  JM [auth A2],  JN [auth G2],  KC [auth 51],  KD [auth 51],  KE [auth 51],  KF [auth 51],  KG [auth 51],  KH [auth 51],  KI [auth 51],  KJ [auth 51],  KK [auth 81],  KL [auth A2],  KM [auth A2],  KN [auth b2],  LC [auth 51],  LD [auth 51],  LE [auth 51],  LF [auth 51],  LG [auth 51],  LH [auth 51],  LI [auth 51],  LJ [auth 51],  LK [auth A2],  LL [auth A2],  LM [auth A2],  MC [auth 51],  MD [auth 51],  ME [auth 51],  MF [auth 51],  MG [auth 51],  MH [auth 51],  MI [auth 51],  MJ [auth 51],  MK [auth A2],  ML [auth A2],  MM [auth A2],  NC [auth 51],  ND [auth 51],  NE [auth 51],  NF [auth 51],  NG [auth 51],  NH [auth 51],  NI [auth 51],  NJ [auth 51],  NK [auth A2],  NL [auth A2],  NM [auth A2],  NN [auth g2],  OC [auth 51],  OD [auth 51],  OE [auth 51],  OF [auth 51],  OG [auth 51],  OH [auth 51],  OI [auth 51],  OJ [auth 51],  OK [auth A2],  OL [auth A2],  OM [auth A2],  PC [auth 51],  PD [auth 51],  PE [auth 51],  PF [auth 51],  PG [auth 51],  PH [auth 51],  PI [auth 51],  PJ [auth 51],  PK [auth A2],  PL [auth A2],  PM [auth A2],  PN [auth B3],  QC [auth 51],  QD [auth 51],  QE [auth 51],  QF [auth 51],  QG [auth 51],  QH [auth 51],  QI [auth 51],  QJ [auth 51],  QK [auth A2],  QL [auth A2],  QM [auth A2],  QN [auth B3],  RC [auth 51],  RD [auth 51],  RE [auth 51],  RF [auth 51],  RG [auth 51],  RH [auth 51],  RI [auth 51],  RJ [auth 51],  RK [auth A2],  RL [auth A2],  RM [auth A2],  RN [auth D3],  SC [auth 51],  SD [auth 51],  SE [auth 51],  SF [auth 51],  SG [auth 51],  SH [auth 51],  SI [auth 51],  SJ [auth 51],  SK [auth A2],  SL [auth A2],  SM [auth A2],  SN [auth N3],  TC [auth 51],  TD [auth 51],  TE [auth 51],  TF [auth 51],  TG [auth 51],  TH [auth 51],  TI [auth 51],  TJ [auth 51],  TK [auth A2],  TL [auth A2],  TM [auth A2],  TN [auth P3],  UC [auth 51],  UD [auth 51],  UE [auth 51],  UF [auth 51],  UG [auth 51],  UH [auth 51],  UI [auth 51],  UJ [auth 51],  UK [auth A2],  UL [auth A2],  UM [auth A2],  UN [auth V3],  VC [auth 51],  VD [auth 51],  VE [auth 51],  VF [auth 51],  VG [auth 51],  VH [auth 51],  VI [auth 51],  VJ [auth 51],  VK [auth A2],  VL [auth A2],  VM [auth A2],  VN [auth a3],  WC [auth 51],  WD [auth 51],  WE [auth 51],  WF [auth 51],  WG [auth 51],  WH [auth 51],  WI [auth 51],  WJ [auth 51],  WK [auth A2],  WL [auth A2],  WM [auth A2],  WN [auth e3],  XC [auth 51],  XD [auth 51],  XE [auth 51],  XF [auth 51],  XG [auth 51],  XH [auth 51],  XI [auth 51],  XJ [auth 51],  XK [auth A2],  XL [auth A2],  XM [auth A2],  YC [auth 51],  YD [auth 51],  YE [auth 51],  YF [auth 51],  YG [auth 51],  YH [auth 51],  YI [auth 51],  YJ [auth 51],  YK [auth A2],  YL [auth A2],  YM [auth A2],  ZC [auth 51],  ZD [auth 51],  ZE [auth 51],  ZF [auth 51],  ZG [auth 51],  ZH [auth 51],  ZI [auth 51],  ZJ [auth 71],  ZK [auth A2],  ZL [auth A2],  ZM [auth A2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 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