9D58 | pdb_00009d58

Human Dystrophin tandem calponin homology actin-binding domain crystallized in a closed-state conformation

• PDB DOI: https://doi.org/10.2210/pdb9D58/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-13 Released: 2025-03-12 
• Deposition Author(s): Streeter, O., Shi, K., Ervasti, J.M., Evans III, R.L., Muretta, J.M.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.262 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: in silico

Literature

Human dystrophin tandem calponin homology actin-binding domain crystallized in a closed-state conformation.

Streeter, O., Shi, K., Vavra, J., Aihara, H., Ervasti, J.M., Evans 3rd, R., Muretta, J.M.

(2025) Acta Crystallogr D Struct Biol 81: 122-129

• PubMed: 40007458 
• DOI: https://doi.org/10.1107/S2059798325001457
• Primary Citation of Related Structures:  
  9D58


• PubMed Abstract: 
  

  The structure of the N-terminal actin-binding domain of human dystrophin was determined at 1.94 Å resolution. Each chain in the asymmetric unit exists in a `closed' conformation, with the first and second calponin homology (CH) domains directly interacting via a 2500.6 Å <sup>2</sup> interface. The positioning of the individual CH domains is comparable to the domain-swapped dimer seen in previous human dystrophin and utrophin actin-binding domain 1 structures. The CH1 domain is highly similar to the actin-bound utrophin structure and structural homology suggests that the `closed' single-chain conformation opens during actin binding to mitigate steric clashes between CH2 and actin.

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Organizational Affiliation: 
• Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 114.29 kDa 
• Atom Count: 7,475 
• Modeled Residue Count: 926 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dystrophin	A, B, C, D	248	Homo sapiens	Mutation(s): 0  Gene Names: DMD
UniProt & NIH Common Fund Data Resources
Find proteins for P11532 (Homo sapiens) Explore P11532  Go to UniProtKB:  P11532
PHAROS:  P11532 GTEx:  ENSG00000198947

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.262 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.774	α = 90
b = 143.138	β = 102.21
c = 59.862	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Streeter, O., Shi, K., Ervasti, J.M., Evans III, R.L., Muretta, J.M.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release