1V9D | pdb_00001v9d

Crystal structure of the core FH2 domain of mouse mDia1

• PDB DOI: https://doi.org/10.2210/pdb1V9D/pdb

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


• Deposited: 2004-01-24 Released: 2004-03-09 
• Deposition Author(s): Shimada, A., Nyitrai, M., Vetter, I.R., Kuhlmann, D., Bugyi, B., Narumiya, S., Geeves, M.A., Wittinghofer, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.267 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.236 (Depositor) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

The core FH2 domain of diaphanous-related formins is an elongated actin binding protein that inhibits polymerization.

Shimada, A., Nyitrai, M., Vetter, I.R., Kuhlmann, D., Bugyi, B., Narumiya, S., Geeves, M.A., Wittinghofer, A.

(2004) Mol Cell 13: 511-522

• PubMed: 14992721 
• DOI: https://doi.org/10.1016/s1097-2765(04)00059-0
• Primary Citation Related Structures: 
  1V9D


• PubMed Abstract: 
  

  Diaphanous-related formins (Drf) are activated by Rho GTP binding proteins and induce polymerization of unbranched actin filaments. They contain three formin homology domains. Evidence as to the effect of formins on actin polymerization were obtained using FH2/FH1 constructs of various length from different Drfs. Here we define the core FH2 domain as a proteolytically stable domain of approximately 338 residues. The monomeric FH2 domains from mDia1 and mDia3 inhibit polymerization of actin and can bind in a 1:1 complex with F-actin at micromolar concentrations. The X-ray structure analysis of the domain shows an elongated, crescent-shaped molecule consisting of three helical subdomains. The most highly conserved regions of the domain span a distance of 75 A and are both required for barbed-end inhibition. A construct containing an additional 72 residue linker has dramatically different properties: It oligomerizes and induces actin polymerization at subnanomolar concentration.

---

Organizational Affiliation: 
• Max-Planck Institut für Molekulare Physiologie, Otto Hahn Strasse 11, D-44227 Dortmund, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 158.4 kDa 
• Atom Count: 10,079 
• Modeled Residue Count: 1,207 
• Deposited Residue Count: 1,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaphanous protein homolog 1	A, B, C, D	340	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O08808 (Mus musculus) Explore O08808  Go to UniProtKB:  O08808
IMPC:  MGI:1194490

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth B], G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.267 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.236 (Depositor) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.43	α = 90
b = 124.521	β = 90
c = 229.404	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-09 
Deposition Author(s): Shimada, A., Nyitrai, M., Vetter, I.R., Kuhlmann, D., Bugyi, B., Narumiya, S., Geeves, M.A., Wittinghofer, A.

Revision History  

• Version 1.0: 2004-03-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations