1QFH

DIMERIZATION OF GELATION FACTOR FROM DICTYOSTELIUM DISCOIDEUM: CRYSTAL STRUCTURE OF ROD DOMAINS 5 AND 6

• PDB DOI: https://doi.org/10.2210/pdb1QFH/pdb

• Classification: ACTIN BINDING PROTEIN
• Organism(s): Dictyostelium discoideum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-04-11 Released: 1999-04-16 
• Deposition Author(s): Mccoy, A.J., Fucini, P., Noegel, A.A., Stewart, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.267 
• R-Value Work: 0.222 
• R-Value Observed: 0.219 

Literature

Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod.

McCoy, A.J., Fucini, P., Noegel, A.A., Stewart, M.

(1999) Nat Struct Biol 6: 836-841

• PubMed: 10467095 
• DOI: https://doi.org/10.1038/12296
• Primary Citation of Related Structures:  
  1QFH


• PubMed Abstract: 
  

  Gelation factor (ABP120) is one of the principal actin-cross-linking proteins of Dictyostelium discoideum. The extended molecule has an N-terminal 250-residue actin-binding domain and a rod constructed from six 100-residue repeats that have an Ig fold. The ability to dimerize is crucial to the actin cross-linking function of gelation factor and is mediated by the rod in which the two chains are arranged in an antiparallel fashion. We report the 2.2 A resolution crystal structure of rod domains 5 and 6, which shows that dimerization is mediated primarily by rod domain 6 and is the result of a double edge-to-edge extension of beta-sheets. Thus, contrary to earlier proposals, the chains of the dimeric gelation factor molecule overlap only within domain 6, and domains 1-5 do not pair with domains from the other chain. This information allows construction of a model of the gelation factor molecule and suggests how the chains in the related molecule filamin (ABP280) may interact.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Hills Rd, Cambridge CB2 2QH, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 44.71 kDa 
• Atom Count: 3,337 
• Modelled Residue Count: 424 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GELATION FACTOR)	A, B	212	Dictyostelium discoideum	Mutation(s): 0
UniProt
Find proteins for P13466 (Dictyostelium discoideum) Explore P13466  Go to UniProtKB:  P13466

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.267 
• R-Value Work: 0.222 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.448	α = 90
b = 103.15	β = 90
c = 124.361	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-16 
Deposition Author(s): Mccoy, A.J., Fucini, P., Noegel, A.A., Stewart, M.

Revision History  

• Version 1.0: 1999-04-16
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-27
  Changes: Database references
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references