5CK3 | pdb_00005ck3

Signal recognition particle receptor SRb-GTP/SRX complex from Chaetomium thermophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.300 (Depositor), 0.302 (DCC) 
  • R-Value Work: 
    0.276 (Depositor), 0.277 (DCC) 
  • R-Value Observed: 
    0.278 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure and Switch Cycle of SR beta as Ancestral Eukaryotic GTPase Associated with Secretory Membranes.

Jadhav, B.Wild, K.Pool, M.R.Sinning, I.

(2015) Structure 23: 1838-1847

  • DOI: https://doi.org/10.1016/j.str.2015.07.010
  • Primary Citation Related Structures: 
    5CK3, 5CK4, 5CK5

  • PubMed Abstract: 

    G proteins of the Ras-family of small GTPases trace the evolution of eukaryotes. The earliest branching involves the closely related Arf, Sar1, and SRβ GTPases associated with secretory membranes. SRβ is an integral membrane component of the signal recognition particle (SRP) receptor that targets ribosome-nascent chain complexes to the ER. How SRβ integrates into the regulation of SRP-dependent membrane protein biogenesis is not known. Here we show that SRβ-GTP interacts with ribosomes only in presence of SRα and present crystal structures of SRβ in complex with the SRX domain of SRα in the GTP-bound state at 3.2 Å, and of GDP- and GDP · Mg(2+)-bound SRβ at 1.9 Å and 2.4 Å, respectively. We define the GTPase switch cycle of SRβ and identify specific differences to the Arf and Sar1 families with implications for GTPase regulation. Our data allow a better integration of SRβ into the scheme of protein targeting.


  • Organizational Affiliation
    • Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany; Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK.

Macromolecule Content 

  • Total Structure Weight: 163.29 kDa 
  • Atom Count: 7,900 
  • Modeled Residue Count: 991 
  • Deposited Residue Count: 1,464 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SRX domain
A, C, E
181Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0014570
EC: 2.7.11.1
UniProt
Find proteins for G0S1R8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S1R8 
Go to UniProtKB:  G0S1R8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S1R8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative signal recognition particle protein
B, D, F
307Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0022040
UniProt
Find proteins for G0S401 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S401 
Go to UniProtKB:  G0S401
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S401
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP



Download:Ideal Coordinates CCD File
H [auth B],
L [auth D],
N [auth F]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth B],
K [auth D],
M [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.300 (Depositor), 0.302 (DCC) 
  • R-Value Work:  0.276 (Depositor), 0.277 (DCC) 
  • R-Value Observed: 0.278 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.277α = 90
b = 83.609β = 105.23
c = 90.213γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description