2I2Q | pdb_00002i2q

Fission Yeast cofilin

• PDB DOI: https://doi.org/10.2210/pdb2I2Q/pdb

• Classification: actin-binding protein
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-16 Released: 2006-10-17 
• Deposition Author(s): Andrianantoandro, E., Pollard, T.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.256 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Mechanism of Actin Filament Turnover by Severing and Nucleation at Different Concentrations of ADF/Cofilin.

Andrianantoandro, E., Pollard, T.D.

(2006) Mol Cell 24: 13-23

• PubMed: 17018289 
• DOI: https://doi.org/10.1016/j.molcel.2006.08.006
• Primary Citation Related Structures: 
  2I2Q


• PubMed Abstract: 
  

  ADF/cofilins are key regulators of actin dynamics during cellular motility, yet their precise role and mechanism of action are shrouded in ambiguity. Direct observation of actin filaments by evanescent wave microscopy showed that cofilins from fission yeast and human do not increase the rate that pointed ends of actin filaments shorten beyond the rate for ADP-actin subunits, but both cofilins inhibit elongation and subunit dissociation at barbed ends. Direct observation also showed that cofilins from fission yeast, Acanthamoeba, and human sever actin filaments optimally at low-cofilin binding densities well below their K(d)s, but not at high binding densities. High concentrations of cofilin nucleate actin assembly. Thus, the action of cofilins in cells will depend on the local concentration of active cofilins: low concentrations favor severing, whereas high concentrations favor nucleation. These results establish a clear paradigm for actin turnover by cofilin in cells.

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Organizational Affiliation: 
• Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.31 kDa 
• Atom Count: 1,106 
• Modeled Residue Count: 122 
• Deposited Residue Count: 137 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cofilin	A	137	Schizosaccharomyces pombe	Mutation(s): 0  Gene Names: cof1
UniProt
Find proteins for P78929 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P78929  Go to UniProtKB:  P78929

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LDA	D [auth A]	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.256 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.915	α = 90
b = 81.915	β = 90
c = 61.863	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Andrianantoandro, E., Pollard, T.D.

Revision History  

• Version 1.0: 2006-10-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description