1IZN

Crystal Structure of Actin Filament Capping Protein CapZ

• PDB DOI: https://doi.org/10.2210/pdb1IZN/pdb

• Classification: PROTEIN BINDING
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-10-10 Released: 2003-04-08 
• Deposition Author(s): Yamashita, A., Maeda, K., Maeda, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.262 
• R-Value Work: 0.222 

Literature

Crystal structure of CapZ: structural basis for actin filament barbed end capping

Yamashita, A., Maeda, K., Maeda, Y.

(2003) EMBO J 22: 1529-1538

• PubMed: 12660160 
• DOI: https://doi.org/10.1093/emboj/cdg167


• PubMed Abstract: 
  

  Capping protein, a heterodimeric protein composed of alpha and beta subunits, is a key cellular component regulating actin filament assembly and organization. It binds to the barbed ends of the filaments and works as a 'cap' by preventing the addition and loss of actin monomers at the end. Here we describe the crystal structure of the chicken sarcomeric capping protein CapZ at 2.1 A resolution. The structure shows a striking resemblance between the alpha and beta subunits, so that the entire molecule has a pseudo 2-fold rotational symmetry. CapZ has a pair of mobile extensions for actin binding, one of which also provides concomitant binding to another protein for the actin filament targeting. The mobile extensions probably form flexible links to the end of the actin filament with a pseudo 2(1) helical symmetry, enabling the docking of the two in a symmetry mismatch.

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Organizational Affiliation: 

Laboratory for Structural Biochemistry, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki, Sayo, Hyogo, 679-5148, Japan. [e-mail]

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: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 129.06 kDa 
• Atom Count: 9,272 
• Modelled Residue Count: 1,088 
• Deposited Residue Count: 1,126 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CapZ alpha-1 subunit	A, C	286	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P13127 (Gallus gallus) Explore P13127  Go to UniProtKB:  P13127

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CapZ beta-1 subunit	B, D	277	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P14315 (Gallus gallus) Explore P14315  Go to UniProtKB:  P14315

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	E [auth B], F [auth B], G [auth D], H [auth D]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.262 
• R-Value Work: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.2	α = 90
b = 57.2	β = 113
c = 99.2	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-08 
Deposition Author(s): Yamashita, A., Maeda, K., Maeda, Y.

Revision History  

• Version 1.0: 2003-04-08
  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