4Z8Y

Crystal structure of Rab GTPase Sec4p mutant - S29V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

New insights into the molecular mechanism of the Rab GTPase Sec4p activation.

Rinaldi, F.C.Packer, M.Collins, R.

(2015) Bmc Struct.Biol. 15: 14-14

  • DOI: 10.1186/s12900-015-0041-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sec4p is a small monomeric Ras-related GTP-binding protein (23┬ákDa) that regulates polarized exocytosis in S. cerevisiae. In this study we examine the structural effects of a conserved serine residue in the P-loop corresponding to G12 in Ras.

    Sec4p is a small monomeric Ras-related GTP-binding protein (23 kDa) that regulates polarized exocytosis in S. cerevisiae. In this study we examine the structural effects of a conserved serine residue in the P-loop corresponding to G12 in Ras.


    Organizational Affiliation

    Honors Program in Undergraduate Studies, Cornell University, Ithaca, NY, 14853, USA. michaelpacker@fas.harvard.edu.,Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA. ruth.collins@cornell.edu.,Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA. fcr23@cornell.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein SEC4
A, B
170Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: SEC4 (SRO6)
Find proteins for P07560 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07560
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 31.720α = 90.00
b = 75.450β = 91.58
c = 66.230γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release