5GAD

RNC-SRP-SR complex early state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon.

Jomaa, A.Boehringer, D.Leibundgut, M.Ban, N.

(2016) Nat Commun 7: 10471-10471

  • DOI: 10.1038/ncomms10471
  • Primary Citation of Related Structures:  
    5GAH, 5GAG, 5GAD, 5GAF, 5GAE

  • PubMed Abstract: 
  • Co-translational protein targeting to membranes is a universally conserved process. Central steps include cargo recognition by the signal recognition particle and handover to the Sec translocon. Here we present snapshots of key co-translational-targeting complexes solved by cryo-electron microscopy at near-atomic resolution, establishing the molecular contacts between the Escherichia coli translating ribosome, the signal recognition particle and the translocon ...

    Co-translational protein targeting to membranes is a universally conserved process. Central steps include cargo recognition by the signal recognition particle and handover to the Sec translocon. Here we present snapshots of key co-translational-targeting complexes solved by cryo-electron microscopy at near-atomic resolution, establishing the molecular contacts between the Escherichia coli translating ribosome, the signal recognition particle and the translocon. Our results reveal the conformational changes that regulate the latching of the signal sequence, the release of the heterodimeric domains of the signal recognition particle and its receptor, and the handover of the signal sequence to the translocon. We also observe that the signal recognition particle and the translocon insert-specific structural elements into the ribosomal tunnel to remodel it, possibly to sense nascent chains. Our work provides structural evidence for a conformational state of the signal recognition particle and its receptor primed for translocon binding to the ribosome-nascent chain complex.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich CH-8093, Switzerland.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2E [auth C]273Escherichia coliMutation(s): 0 
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50S ribosomal protein L3F [auth D]209Escherichia coliMutation(s): 0 
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Entity ID: 7
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50S ribosomal protein L4G [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 8
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50S ribosomal protein L5H [auth F]179Escherichia coliMutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L6I [auth G]177Escherichia coliMutation(s): 0 
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Entity ID: 10
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50S ribosomal protein L9J [auth H]149Escherichia coliMutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L10K [auth I]165Escherichia coliMutation(s): 0 
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50S ribosomal protein L11L [auth J]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L13M [auth K]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14N [auth L]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15O [auth M]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16P [auth N]136Escherichia coliMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L17Q [auth O]127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18R [auth P]117Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L19S [auth Q]115Escherichia coliMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L20T [auth R]118Escherichia coliMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L21U [auth S]103Escherichia coliMutation(s): 0 
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Entity ID: 22
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50S ribosomal protein L22V [auth T]110Escherichia coliMutation(s): 0 
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Entity ID: 23
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50S ribosomal protein L23W [auth U]100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24X [auth V]104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25Y [auth W]94Escherichia coliMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L27Z [auth X]85Escherichia coliMutation(s): 0 
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Entity ID: 27
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50S ribosomal protein L28AA [auth Y]78Escherichia coliMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L29BA [auth Z]63Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L30CA [auth a]59Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L32DA [auth b]57Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L33EA [auth c]55Escherichia coliMutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L34FA [auth d]46Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L35GA [auth e]65Escherichia coliMutation(s): 0 
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Entity ID: 34
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50S ribosomal protein L36HA [auth f]38Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle protein FfhIA [auth i]450Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
1A9L SSJA [auth k]18Escherichia coliMutation(s): 0 
EC: 3.1.3.1
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Entity ID: 37
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Signal recognition particle receptor FtsYKA [auth l]497Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
ESRP 4.5S RNAA [auth 1]113Escherichia coli
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    tRNA CCAendB [auth 2]3Escherichia coli
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    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    23S rRNAC [auth A]2903Escherichia coli
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    Entity ID: 4
    MoleculeChainsLengthOrganismImage
    5S rRNAD [auth B]120Escherichia coli
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GNP
    Query on GNP

    Download Ideal Coordinates CCD File 
    BR [auth i], DR [auth l]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
    C10 H17 N6 O13 P3
    UQABYHGXWYXDTK-UUOKFMHZSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    AR [auth f]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , AF [auth A] , AG [auth A] , AH [auth A] , AI [auth A] , 
    AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  AF [auth A],  AG [auth A],  AH [auth A],  AI [auth A],  AJ [auth A],  AK [auth A],  AL [auth A],  AM [auth A],  AN [auth A],  AO [auth A],  AP [auth A],  AQ [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  BE [auth A],  BF [auth A],  BG [auth A],  BH [auth A],  BI [auth A],  BJ [auth A],  BK [auth A],  BL [auth A],  BM [auth A],  BN [auth A],  BO [auth A],  BP [auth A],  BQ [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  CF [auth A],  CG [auth A],  CH [auth A],  CI [auth A],  CJ [auth A],  CK [auth A],  CL [auth A],  CM [auth A],  CN [auth A],  CO [auth A],  CP [auth A],  CQ [auth A],  CR [auth i],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  DF [auth A],  DG [auth A],  DH [auth A],  DI [auth A],  DJ [auth A],  DK [auth A],  DL [auth A],  DM [auth A],  DN [auth A],  DO [auth A],  DP [auth A],  DQ [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  EE [auth A],  EF [auth A],  EG [auth A],  EH [auth A],  EI [auth A],  EJ [auth A],  EK [auth A],  EL [auth A],  EM [auth A],  EN [auth A],  EO [auth A],  EP [auth A],  EQ [auth A],  ER [auth l],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  FF [auth A],  FG [auth A],  FH [auth A],  FI [auth A],  FJ [auth A],  FK [auth A],  FL [auth A],  FM [auth A],  FN [auth A],  FO [auth A],  FP [auth A],  FQ [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  GF [auth A],  GG [auth A],  GH [auth A],  GI [auth A],  GJ [auth A],  GK [auth A],  GL [auth A],  GM [auth A],  GN [auth A],  GO [auth A],  GP [auth A],  GQ [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  HF [auth A],  HG [auth A],  HH [auth A],  HI [auth A],  HJ [auth A],  HK [auth A],  HL [auth A],  HM [auth A],  HN [auth A],  HO [auth A],  HP [auth A],  HQ [auth A],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  IF [auth A],  IG [auth A],  IH [auth A],  II [auth A],  IJ [auth A],  IK [auth A],  IL [auth A],  IM [auth A],  IN [auth A],  IO [auth A],  IP [auth A],  IQ [auth B],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth A],  JF [auth A],  JG [auth A],  JH [auth A],  JI [auth A],  JJ [auth A],  JK [auth A],  JL [auth A],  JM [auth A],  JN [auth A],  JO [auth A],  JP [auth A],  JQ [auth B],  KB [auth A],  KC [auth A],  KD [auth A],  KE [auth A],  KF [auth A],  KG [auth A],  KH [auth A],  KI [auth A],  KJ [auth A],  KK [auth A],  KL [auth A],  KM [auth A],  KN [auth A],  KO [auth A],  KP [auth A],  KQ [auth B],  LA [auth 2],  LB [auth A],  LC [auth A],  LD [auth A],  LE [auth A],  LF [auth A],  LG [auth A],  LH [auth A],  LI [auth A],  LJ [auth A],  LK [auth A],  LL [auth A],  LM [auth A],  LN [auth A],  LO [auth A],  LP [auth A],  LQ [auth B],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  ME [auth A],  MF [auth A],  MG [auth A],  MH [auth A],  MI [auth A],  MJ [auth A],  MK [auth A],  ML [auth A],  MM [auth A],  MN [auth A],  MO [auth A],  MP [auth A],  MQ [auth B],  NA [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  NE [auth A],  NF [auth A],  NG [auth A],  NH [auth A],  NI [auth A],  NJ [auth A],  NK [auth A],  NL [auth A],  NM [auth A],  NN [auth A],  NO [auth A],  NP [auth A],  NQ [auth B],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  OE [auth A],  OF [auth A],  OG [auth A],  OH [auth A],  OI [auth A],  OJ [auth A],  OK [auth A],  OL [auth A],  OM [auth A],  ON [auth A],  OO [auth A],  OP [auth A],  OQ [auth B],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  PE [auth A],  PF [auth A],  PG [auth A],  PH [auth A],  PI [auth A],  PJ [auth A],  PK [auth A],  PL [auth A],  PM [auth A],  PN [auth A],  PO [auth A],  PP [auth A],  PQ [auth B],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  QE [auth A],  QF [auth A],  QG [auth A],  QH [auth A],  QI [auth A],  QJ [auth A],  QK [auth A],  QL [auth A],  QM [auth A],  QN [auth A],  QO [auth A],  QP [auth A],  QQ [auth B],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  RE [auth A],  RF [auth A],  RG [auth A],  RH [auth A],  RI [auth A],  RJ [auth A],  RK [auth A],  RL [auth A],  RM [auth A],  RN [auth A],  RO [auth A],  RP [auth A],  RQ [auth B],  SA [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  SE [auth A],  SF [auth A],  SG [auth A],  SH [auth A],  SI [auth A],  SJ [auth A],  SK [auth A],  SL [auth A],  SM [auth A],  SN [auth A],  SO [auth A],  SP [auth A],  SQ [auth B],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  TE [auth A],  TF [auth A],  TG [auth A],  TH [auth A],  TI [auth A],  TJ [auth A],  TK [auth A],  TL [auth A],  TM [auth A],  TN [auth A],  TO [auth A],  TP [auth A],  TQ [auth C],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  UE [auth A],  UF [auth A],  UG [auth A],  UH [auth A],  UI [auth A],  UJ [auth A],  UK [auth A],  UL [auth A],  UM [auth A],  UN [auth A],  UO [auth A],  UP [auth A],  UQ [auth C],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  VE [auth A],  VF [auth A],  VG [auth A],  VH [auth A],  VI [auth A],  VJ [auth A],  VK [auth A],  VL [auth A],  VM [auth A],  VN [auth A],  VO [auth A],  VP [auth A],  VQ [auth D],  WA [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  WE [auth A],  WF [auth A],  WG [auth A],  WH [auth A],  WI [auth A],  WJ [auth A],  WK [auth A],  WL [auth A],  WM [auth A],  WN [auth A],  WO [auth A],  WP [auth A],  WQ [auth E],  XA [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  XE [auth A],  XF [auth A],  XG [auth A],  XH [auth A],  XI [auth A],  XJ [auth A],  XK [auth A],  XL [auth A],  XM [auth A],  XN [auth A],  XO [auth A],  XP [auth A],  XQ [auth P],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  YE [auth A],  YF [auth A],  YG [auth A],  YH [auth A],  YI [auth A],  YJ [auth A],  YK [auth A],  YL [auth A],  YM [auth A],  YN [auth A],  YO [auth A],  YP [auth A],  YQ [auth R],  ZA [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A],  ZE [auth A],  ZF [auth A],  ZG [auth A],  ZH [auth A],  ZI [auth A],  ZJ [auth A],  ZK [auth A],  ZL [auth A],  ZM [auth A],  ZN [auth A],  ZO [auth A],  ZP [auth A],  ZQ [auth b]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.70 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: 2016-01-27
      Type: Initial release
    • Version 1.1: 2016-02-03
      Changes: Database references
    • Version 1.2: 2017-08-30
      Changes: Data collection
    • Version 1.3: 2019-11-06
      Changes: Data collection
    • Version 1.4: 2019-12-11
      Changes: Other