4ZDW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    4Z8Y, 4ZDW

  • PubMed Abstract: 
  • 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

    Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA. ruth.collins@cornell.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein SEC4A170Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: SEC4SRO6YFL005W
UniProt
Find proteins for P07560 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07560 
Go to UniProtKB:  P07560
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Rab guanine nucleotide exchange factor SEC2B, C93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SEC2YNL272CN0641
UniProt
Find proteins for P17065 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17065 
Go to UniProtKB:  P17065
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
D [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.9α = 90
b = 119.28β = 90
c = 122.86γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM069596

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence