2ZWH | pdb_00002zwh

Model for the F-actin structure

• PDB DOI: https://doi.org/10.2210/pdb2ZWH/pdb

• Classification: CONTRACTILE PROTEIN
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2008-12-05 Released: 2009-01-20 
• Deposition Author(s): Oda, T., Iwasa, M., Aihara, T., Maeda, Y., Narita, A.

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Experimental Data Snapshot

• Method: FIBER DIFFRACTION
• Resolution: 3.30 Å

Literature

The nature of the globular- to fibrous-actin transition.

Oda, T., Iwasa, M., Aihara, T., Maeda, Y., Narita, A.

(2009) Nature 457: 441-445

• PubMed: 19158791 
• DOI: https://doi.org/10.1038/nature07685
• Primary Citation Related Structures: 
  2ZWH


• PubMed Abstract: 
  

  Actin plays crucial parts in cell motility through a dynamic process driven by polymerization and depolymerization, that is, the globular (G) to fibrous (F) actin transition. Although our knowledge about the actin-based cellular functions and the molecules that regulate the G- to F-actin transition is growing, the structural aspects of the transition remain enigmatic. We created a model of F-actin using X-ray fibre diffraction intensities obtained from well oriented sols of rabbit skeletal muscle F-actin to 3.3 A in the radial direction and 5.6 A along the equator. Here we show that the G- to F-actin conformational transition is a simple relative rotation of the two major domains by about 20 degrees. As a result of the domain rotation, the actin molecule in the filament is flat. The flat form is essential for the formation of stable, helical F-actin. Our F-actin structure model provides the basis for understanding actin polymerization as well as its molecular interactions with actin-binding proteins.

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Organizational Affiliation: 
• X-ray Structural Analysis Research Team, RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.34 kDa 
• Atom Count: 2,961 
• Modeled Residue Count: 375 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A	375	Oryctolagus cuniculus	Mutation(s): 0  EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: FIBER DIFFRACTION
• Resolution: 3.30 Å

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 1	α = 90
b = 1	β = 90
c = 1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Oda, T., Iwasa, M., Aihara, T., Maeda, Y., Narita, A.

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2015-02-11
  Changes: Other
• Version 1.3: 2015-10-14
  Changes: Refinement description
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 1.5: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary