9DYQ | pdb_00009dyq

Crystal structure of human dysferlin C2G domain

• PDB DOI: https://doi.org/10.2210/pdb9DYQ/pdb

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


• Deposited: 2024-10-14 Released: 2025-10-22 
• Deposition Author(s): Dominguez, M.J., Sutton, R.B.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.273 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of human dysferlin C2G domain

Dominguez, M.J., Sutton, R.B.

To be published.

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.

Macromolecule Content 

• Total Structure Weight: 47.57 kDa 
• Atom Count: 3,379 
• Modeled Residue Count: 388 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dysferlin	A, B	200	Homo sapiens	Mutation(s): 0  Gene Names: DYSF, FER1L1
UniProt & NIH Common Fund Data Resources
Find proteins for O75923 (Homo sapiens) Explore O75923  Go to UniProtKB:  O75923
PHAROS:  O75923 GTEx:  ENSG00000135636

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	G [auth A], N [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A], L [auth B], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.273 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.942	α = 90
b = 109.76	β = 90
c = 59.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Dominguez, M.J., Sutton, R.B.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release
  
• Version 1.1: 2025-10-29
  Changes: Source and taxonomy
• Version 2.0: 2025-12-03
  Changes: Advisory, Database references, Polymer sequence, Source and taxonomy, Structure summary