7OBQ

SRP-SR at the distal site conformation

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

  • 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: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle 19B [auth q]144Canis lupus familiarisMutation(s): 0 
Gene Names: SRP19
UniProt
Find proteins for J9PAS6 (Canis lupus familiaris)
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UniProt GroupJ9PAS6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
EM14S01-3B_G0054400.mRNA.1.CDS.1C [auth s]62Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS2833
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP68,Signal recognition particle subunit SRP68D [auth u]622Canis lupus familiarisMutation(s): 0 
Gene Names: SRP68
UniProt
Find proteins for Q00004 (Canis lupus familiaris)
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UniProt GroupQ00004
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle receptor subunit betaE [auth v]271Oryctolagus cuniculusMutation(s): 0 
Gene Names: SRPRB
UniProt
Find proteins for G1STG2 (Oryctolagus cuniculus)
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UniProt GroupG1STG2
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle 54 kDa proteinF [auth x]504Canis lupus familiarisMutation(s): 0 
Gene Names: SRP54
EC: 3.6.5
UniProt
Find proteins for P61010 (Canis lupus familiaris)
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UniProt GroupP61010
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
SRP receptor subunit alphaG [auth y]637Oryctolagus cuniculusMutation(s): 0 
Gene Names: SRPRA
UniProt
Find proteins for A0A5F9CI80 (Oryctolagus cuniculus)
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UniProt GroupA0A5F9CI80
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP72H [auth z]671Canis lupus familiarisMutation(s): 0 
Gene Names: SRP72
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
SRP RNAA [auth 1]249Canis lupus familiaris
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP
Download Ideal Coordinates CCD File 
J [auth v]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
GNP (Subject of Investigation/LOI)
Query on GNP
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K [auth x],
M [auth y]		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N		 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
I [auth v],
L [auth x],
N [auth y]		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 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

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