3JAN

Structure of the scanning state of the mammalian SRP-ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 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

Structures of the scanning and engaged states of the mammalian SRP-ribosome complex.

Voorhees, R.M.Hegde, R.S.

(2015) Elife 4

  • DOI: 10.7554/eLife.07975
  • Primary Citation of Related Structures:  
    3JAJ, 3JAN

  • PubMed Abstract: 
  • The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially engaging those with hydrophobic targeting signals, and delivers these ribosome-nascent chain complexes to the membrane ...

    The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially engaging those with hydrophobic targeting signals, and delivers these ribosome-nascent chain complexes to the membrane. Here, we present structures of native mammalian SRP-ribosome complexes in the scanning and engaged states. These structures reveal the near-identical SRP architecture of these two states, show many of the SRP-ribosome interactions at atomic resolution, and suggest how the polypeptide-binding M domain selectively engages hydrophobic signals. The scanning M domain, pre-positioned at the ribosomal exit tunnel, is auto-inhibited by a C-terminal amphipathic helix occluding its hydrophobic binding groove. Upon engagement, the hydrophobic targeting signal displaces this amphipathic helix, which then acts as a protective lid over the signal. Biochemical experiments suggest how scanning and engagement are coordinated with translation elongation to minimize exposure of hydrophobic signals during membrane targeting.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.



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28S ribosomal RNAFA [auth 5]3658Oryctolagus cuniculus
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5.8S ribosomal RNAHA [auth 8]156Oryctolagus cuniculus
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Val tRNAWA [auth 3]76Oryctolagus cuniculus
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18S ribosomal RNAAB [auth S2]1742Oryctolagus cuniculus
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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MH [auth j], NC [auth m], OC [auth o], XI [auth Sa]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 S2] , BD [auth 5] , BE [auth 5] , 
AD [auth 5],  AE [auth 5],  AF [auth 5],  AG [auth 5],  AH [auth 5],  AI [auth S2],  BD [auth 5],  BE [auth 5],  BF [auth 5],  BG [auth 5],  BH [auth 7],  BI [auth S2],  CD [auth 5],  CE [auth 5],  CF [auth 5],  CG [auth 5],  CH [auth 7],  CI [auth S2],  DD [auth 5],  DE [auth 5],  DF [auth 5],  DG [auth 5],  DH [auth 7],  DI [auth S2],  ED [auth 5],  EE [auth 5],  EF [auth 5],  EG [auth 5],  EH [auth 7],  EI [auth S2],  FD [auth 5],  FE [auth 5],  FF [auth 5],  FG [auth 5],  FH [auth 7],  FI [auth S2],  GD [auth 5],  GE [auth 5],  GF [auth 5],  GG [auth 5],  GH [auth 8],  GI [auth S2],  HD [auth 5],  HE [auth 5],  HF [auth 5],  HG [auth 5],  HH [auth 8],  HI [auth S2],  ID [auth 5],  IE [auth 5],  IF [auth 5],  IG [auth 5],  IH [auth 8],  II [auth S2],  JD [auth 5],  JE [auth 5],  JF [auth 5],  JG [auth 5],  JH [auth 8],  JI [auth S2],  KC [auth D],  KD [auth 5],  KE [auth 5],  KF [auth 5],  KG [auth 5],  KH [auth 8],  KI [auth S2],  LC [auth V],  LD [auth 5],  LE [auth 5],  LF [auth 5],  LG [auth 5],  LH [auth 8],  LI [auth S2],  MC [auth g],  MD [auth 5],  ME [auth 5],  MF [auth 5],  MG [auth 5],  MI [auth S2],  ND [auth 5],  NE [auth 5],  NF [auth 5],  NG [auth 5],  NH [auth S2],  NI [auth S2],  OD [auth 5],  OE [auth 5],  OF [auth 5],  OG [auth 5],  OH [auth S2],  OI [auth S2],  PC [auth 5],  PD [auth 5],  PE [auth 5],  PF [auth 5],  PG [auth 5],  PH [auth S2],  PI [auth S2],  QC [auth 5],  QD [auth 5],  QE [auth 5],  QF [auth 5],  QG [auth 5],  QH [auth S2],  QI [auth S2],  RC [auth 5],  RD [auth 5],  RE [auth 5],  RF [auth 5],  RG [auth 5],  RH [auth S2],  RI [auth S2],  SC [auth 5],  SD [auth 5],  SE [auth 5],  SF [auth 5],  SG [auth 5],  SH [auth S2],  SI [auth S2],  TC [auth 5],  TD [auth 5],  TE [auth 5],  TF [auth 5],  TG [auth 5],  TH [auth S2],  TI [auth S2],  UC [auth 5],  UD [auth 5],  UE [auth 5],  UF [auth 5],  UG [auth 5],  UH [auth S2],  UI [auth S2],  VC [auth 5],  VD [auth 5],  VE [auth 5],  VF [auth 5],  VG [auth 5],  VH [auth S2],  VI [auth S2],  WC [auth 5],  WD [auth 5],  WE [auth 5],  WF [auth 5],  WG [auth 5],  WH [auth S2],  WI [auth S2],  XC [auth 5],  XD [auth 5],  XE [auth 5],  XF [auth 5],  XG [auth 5],  XH [auth S2],  YC [auth 5],  YD [auth 5],  YE [auth 5],  YF [auth 5],  YG [auth 5],  YH [auth S2],  ZC [auth 5],  ZD [auth 5],  ZE [auth 5],  ZF [auth 5],  ZG [auth 5],  ZH [auth S2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-12-30
    Changes: Database references