3W6R

Crystal structure of the GAP domain of human MgcRacGAP

• PDB DOI: https://doi.org/10.2210/pdb3W6R/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-21 Released: 2014-02-26 
• Deposition Author(s): Matsuura, A., Lee, H.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.259 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

Crystal structure of GTPase-activating domain from human MgcRacGAP.

Matsuura, A., Lee, H.H.

(2013) Biochem Biophys Res Commun 435: 367-372

• PubMed: 23665020 
• DOI: https://doi.org/10.1016/j.bbrc.2013.04.094
• Primary Citation of Related Structures:  
  3W6R


• PubMed Abstract: 
  

  Cytokinesis in animal cells relies on a centralspindlin complex consisting of male germ cell RacGap (MgcRacGAP) and mitotic kinesin-like protein 1 (MKLP1). Rho GTPases act as molecular switches to regulate the actin cytoskeleton for cytokinesis, of which Rac1 is regulated by MgcRacGAP. In this study, we determined the crystal structure of the GTPase-activating protein (GAP) domain of MgcRacGAP at a resolution of 1.9Å. The conformation of Arg385, which is a key residue for GAP activity, was found to be different from that of previously reported GAP proteins, and MgcRacGAP (residues 348-546) was found to exist as a monomer in solution, according to Stokes radii. We also measured the GAP activity of MgcRacGAP mutants for Rac1.

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Organizational Affiliation: 

Department of Bio & Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.79 kDa 
• Atom Count: 1,717 
• Modelled Residue Count: 200 
• Deposited Residue Count: 202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rac GTPase-activating protein 1	A	202	Homo sapiens	Mutation(s): 0  Gene Names: RACGAP1, KIAA1478, MGCRACGAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0H5 (Homo sapiens) Explore Q9H0H5  Go to UniProtKB:  Q9H0H5
PHAROS:  Q9H0H5 GTEx:  ENSG00000161800

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.259 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.466	α = 90
b = 63.159	β = 90
c = 74.078	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Matsuura, A., Lee, H.H.

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description