4AKR

Crystal Structure of the cytoplasmic actin capping protein Cap32_34 from Dictyostelium discoideum

• PDB DOI: https://doi.org/10.2210/pdb4AKR/pdb

• Classification: ACTIN-BINDING PROTEIN
• Organism(s): Dictyostelium discoideum AX2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-28 Released: 2012-07-04 
• Deposition Author(s): Eckert, C., Goretzki, A., Faberova, M., Kollmar, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.265 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Conservation and Divergence between Cytoplasmic and Muscle-Specific Actin Capping Proteins: Insights from the Crystal Structure of Cytoplasmic CAP32/34 from Dictyostelium Discoideum.

Eckert, C., Goretzki, A., Faberova, M., Kollmar, M.

(2012) BMC Struct Biol 12: 12

• PubMed: 22657106 
• DOI: https://doi.org/10.1186/1472-6807-12-12
• Primary Citation of Related Structures:  
  4AKR


• PubMed Abstract: 
  

  Capping protein (CP), also known as CapZ in muscle cells and Cap32/34 in Dictyostelium discoideum, plays a major role in regulating actin filament dynamics. CP is a ubiquitously expressed heterodimer comprising an α- and β-subunit. It tightly binds to the fast growing end of actin filaments, thereby functioning as a "cap" by blocking the addition and loss of actin subunits. Vertebrates contain two somatic variants of CP, one being primarily found at the cell periphery of non-muscle tissues while the other is mainly localized at the Z-discs of skeletal muscles.

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Organizational Affiliation: 

Abteilung NMR basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077, Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 128.14 kDa 
• Atom Count: 8,399 
• Modelled Residue Count: 1,028 
• Deposited Residue Count: 1,142 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F-ACTIN-CAPPING PROTEIN SUBUNIT ALPHA	A, C	281	Dictyostelium discoideum AX2	Mutation(s): 0
UniProt
Find proteins for P13022 (Dictyostelium discoideum) Explore P13022  Go to UniProtKB:  P13022

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F-ACTIN-CAPPING PROTEIN SUBUNIT BETA	B, D	290	Dictyostelium discoideum AX2	Mutation(s): 0
UniProt
Find proteins for P13021 (Dictyostelium discoideum) Explore P13021  Go to UniProtKB:  P13021

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.265 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.46	α = 90
b = 124.46	β = 90
c = 77.5	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-04 
Deposition Author(s): Eckert, C., Goretzki, A., Faberova, M., Kollmar, M.

Revision History  

• Version 1.0: 2012-07-04
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description