4ZDW

Crystal structure of the Rab GTPase Sec4p mutant - S29V in complex with Sec2p and GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Rab guanine nucleotide exchange factor SEC2
B, C
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SEC2
Find proteins for P17065 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17065
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.258 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 116.900α = 90.00
b = 119.280β = 90.00
c = 122.860γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States5R01GM069596

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Derived calculations
  • Version 1.2: 2017-11-01
    Type: Author supporting evidence