4GYV | pdb_00004gyv

Crystal structure of the DH domain of FARP2

• PDB DOI: https://doi.org/10.2210/pdb4GYV/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-09-05 Released: 2013-03-13 
• Deposition Author(s): He, X., Zhang, X.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.221 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Structural Basis for Autoinhibition of the Guanine Nucleotide Exchange Factor FARP2.

He, X., Kuo, Y.C., Rosche, T.J., Zhang, X.

(2013) Structure 21: 355-364

• PubMed: 23375260 
• DOI: https://doi.org/10.1016/j.str.2013.01.001
• Primary Citation Related Structures: 
  4GYV, 4GZU, 4H6Y


• PubMed Abstract: 
  

  FARP2 is a Dbl-family guanine nucleotide exchange factor (GEF) that contains a 4.1, ezrin, radixin and moesin (FERM) domain, a Dbl-homology (DH) domain and two pleckstrin homology (PH) domains. FARP2 activates Rac1 or Cdc42 in response to upstream signals, thereby regulating processes such as neuronal axon guidance and bone homeostasis. How the GEF activity of FARP2 is regulated remained poorly understood. We have determined the crystal structures of the catalytic DH domain and the DH-PH-PH domains of FARP2. The structures reveal an auto-inhibited conformation in which the GEF substrate-binding site is blocked collectively by the last helix in the DH domain and the two PH domains. This conformation is stabilized by multiple interactions among the domains and two well-structured inter-domain linkers. Our cell-based activity assays confirm the suppression of the FARP2 GEF activity by these auto-inhibitory elements.

---

Organizational Affiliation: 
• Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75063, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 232.11 kDa 
• Atom Count: 15,733 
• Modeled Residue Count: 1,941 
• Deposited Residue Count: 1,962 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FERM, RhoGEF and pleckstrin domain-containing protein 2	A, B, C, D, E, F, G, H, I	218	Mus musculus	Mutation(s): 0  Gene Names: Farp2, Kiaa0793
UniProt & NIH Common Fund Data Resources
Find proteins for Q91VS8 (Mus musculus) Explore Q91VS8  Go to UniProtKB:  Q91VS8
IMPC:  MGI:2385126

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.221 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.193	α = 90
b = 209.991	β = 90
c = 325.009	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-13 
Deposition Author(s): He, X., Zhang, X.

Revision History  

• Version 1.0: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2013-03-27
  Changes: Database references
• Version 1.2: 2016-12-21
  Changes: Structure summary
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary