7OBR

RNC-SRP early complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle.

Jomaa, A.Eitzinger, S.Zhu, Z.Chandrasekar, S.Kobayashi, K.Shan, S.O.Ban, N.

(2021) Cell Rep 36: 109350-109350

  • DOI: 10.1016/j.celrep.2021.109350
  • Primary Citation of Related Structures:  
    7OBR, 7OBQ

  • PubMed Abstract: 
  • Co-translational protein targeting to membranes by the signal recognition particle (SRP) is a universally conserved pathway from bacteria to humans. In mammals, SRP and its receptor (SR) have many additional RNA features and protein components compared to the bacterial system, which were recently shown to play regulatory roles ...

    Co-translational protein targeting to membranes by the signal recognition particle (SRP) is a universally conserved pathway from bacteria to humans. In mammals, SRP and its receptor (SR) have many additional RNA features and protein components compared to the bacterial system, which were recently shown to play regulatory roles. Due to its complexity, the mammalian SRP targeting process is mechanistically not well understood. In particular, it is not clear how SRP recognizes translating ribosomes with exposed signal sequences and how the GTPase activity of SRP and SR is regulated. Here, we present electron cryo-microscopy structures of SRP and SRP·SR in complex with the translating ribosome. The structures reveal the specific molecular interactions between SRP and the emerging signal sequence and the elements that regulate GTPase activity of SRP·SR. Our results suggest the molecular mechanism of how eukaryote-specific elements regulate the early and late stages of SRP-dependent protein targeting.


    Related Citations: 
    • Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle
      Jomaa, A., Eitzinger, S., Zhu, Z., Chandrasekar, S., Kobayashi, K., Shan, S., Ban, N.
      (2021) Cell Rep 36: --

    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland. Electronic address: ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8E [auth A]245Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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Entity ID: 6
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uL3F [auth B]402Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
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Entity ID: 7
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60S ribosomal protein L4G [auth C]413Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
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60S ribosomal protein L5H [auth D]297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
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60S ribosomal protein L6I [auth E]248Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
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uL30J [auth F]225Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
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60S ribosomal protein L7aK [auth G]319Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L9L [auth H]192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
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60S ribosomal protein L10M [auth I]214Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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Entity ID: 14
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Ribosomal protein L11N [auth J]178Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
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Entity ID: 15
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60S ribosomal protein L13O [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
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60S ribosomal protein L14P [auth M]218Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
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Entity ID: 17
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Ribosomal protein L15Q [auth N]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
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60S ribosomal protein L13aR [auth O]199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
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uL22S [auth P]153Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL17-C18orf32
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Entity ID: 20
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eL18T [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
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60S RIBOSOMAL PROTEIN EL19U [auth R]180Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L18aV [auth S]175Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL18A
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Entity ID: 23
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eL21W [auth T]160Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
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Entity ID: 24
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Ribosomal protein L22X [auth U]99Oryctolagus cuniculusMutation(s): 6 
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Entity ID: 25
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Ribosomal protein L23Y [auth V]140Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
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Ribosomal protein L24Z [auth W]63Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
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Entity ID: 27
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uL23AA [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
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Ribosomal protein L26BA [auth Y]145Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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Entity ID: 29
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60S ribosomal protein L27CA [auth Z]136Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27
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Entity ID: 30
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uL15DA [auth a]147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
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60S ribosomal protein L29EA [auth b]223Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
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60S ribosomal protein L30FA [auth c]94Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
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eL31GA [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
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eL32HA [auth e]157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
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eL33IA [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
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60S ribosomal protein L34JA [auth g]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
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uL29KA [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
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60S ribosomal protein L36LA [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
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Ribosomal protein L37MA [auth j]97Oryctolagus cuniculusMutation(s): 0 
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eL38NA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
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eL39OA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN EL40PA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
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60s ribosomal protein l41QA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
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eL42RA [auth o]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
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eL43SA [auth p]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
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Signal recognition particle 19TA [auth q]144Canis lupus familiarisMutation(s): 0 
Gene Names: SRP19
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Entity ID: 47
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eL28UA [auth r]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
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Dipeptidyl aminopeptidase BVA [auth s]67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DAP2YHR028C
EC: 3.4.14
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Entity ID: 49
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Signal recognition particle 14 kDa proteinWA [auth t]110Canis lupus familiarisMutation(s): 0 
Gene Names: SRP14
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Entity ID: 50
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Signal recognition particle subunit SRP68XA [auth u]622Canis lupus familiarisMutation(s): 0 
Gene Names: SRP68
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Entity ID: 51
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Signal recognition particle 9 kDa proteinYA [auth w]86Canis lupus familiarisMutation(s): 0 
Gene Names: SRP9
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Entity ID: 52
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Signal recognition particle 54 kDa proteinZA [auth x]504Canis lupus familiarisMutation(s): 0 
Gene Names: SRP54
EC: 3.6.5
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Entity ID: 53
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Signal recognition particle subunit SRP72AB [auth z]671Canis lupus familiarisMutation(s): 0 
Gene Names: SRP72
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Entity ID: 1
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SRP RNAA [auth 1]249Canis lupus familiaris
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Entity ID: 2
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28S rRNAB [auth 5]3493Oryctolagus cuniculus
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5S ribosomal RNAC [auth 7]120Oryctolagus cuniculus
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Entity ID: 4
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5.8S ribosomal RNAD [auth 8]156Oryctolagus cuniculus
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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ZE [auth x]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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UE [auth g], VE [auth j], WE [auth m], XE [auth o], YE [auth p]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth 5] , AD [auth 5] , AE [auth 5] , BB [auth 5] , BC [auth 5] , BD [auth 5] , BE [auth 5] , CB [auth 5] , 
AC [auth 5],  AD [auth 5],  AE [auth 5],  BB [auth 5],  BC [auth 5],  BD [auth 5],  BE [auth 5],  CB [auth 5],  CC [auth 5],  CD [auth 5],  CE [auth 5],  DB [auth 5],  DC [auth 5],  DD [auth 5],  DE [auth 5],  EB [auth 5],  EC [auth 5],  ED [auth 5],  EE [auth 5],  FB [auth 5],  FC [auth 5],  FD [auth 5],  FE [auth 5],  GB [auth 5],  GC [auth 5],  GD [auth 5],  GE [auth 5],  HB [auth 5],  HC [auth 5],  HD [auth 5],  HE [auth 5],  IB [auth 5],  IC [auth 5],  ID [auth 5],  IE [auth 5],  JB [auth 5],  JC [auth 5],  JD [auth 5],  JE [auth 5],  KB [auth 5],  KC [auth 5],  KD [auth 5],  KE [auth 5],  LB [auth 5],  LC [auth 5],  LD [auth 5],  LE [auth 5],  MB [auth 5],  MC [auth 5],  MD [auth 5],  ME [auth 5],  NB [auth 5],  NC [auth 5],  ND [auth 5],  NE [auth 5],  OB [auth 5],  OC [auth 5],  OD [auth 5],  OE [auth 5],  PB [auth 5],  PC [auth 5],  PD [auth 5],  PE [auth 5],  QB [auth 5],  QC [auth 5],  QD [auth 5],  QE [auth 5],  RB [auth 5],  RC [auth 5],  RD [auth 5],  RE [auth 5],  SB [auth 5],  SC [auth 5],  SD [auth 5],  SE [auth 5],  TB [auth 5],  TC [auth 5],  TD [auth 5],  TE [auth 5],  UB [auth 5],  UC [auth 5],  UD [auth 5],  VB [auth 5],  VC [auth 5],  VD [auth 5],  WB [auth 5],  WC [auth 5],  WD [auth 5],  XB [auth 5],  XC [auth 5],  XD [auth 5],  YB [auth 5],  YC [auth 5],  YD [auth 5],  ZB [auth 5],  ZC [auth 5],  ZD [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-04-23 
  • Released Date: 2021-07-21 
  • Deposition Author(s): Jomaa, A., Ban, N.

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references