4CAH

Structure of inner DysF domain of human dysferlin

PDB DOI: https://doi.org/10.2210/pdb4CAH/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2013-10-08 Released: 2014-01-29
Deposition Author(s): Sula, A., Cole, A.R., Yeats, C., Orengo, C., Keep, N.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.191
R-Value Work: 0.177
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structures of the Human Dysferlin Inner Dysf Domain

Sula, A., Cole, A.R., Yeats, C., Orengo, C., Keep, N.H.

(2014) BMC Struct Biol 14: 3

PubMed: 24438169 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/1472-6807-14-3
Primary Citation of Related Structures:
4CAH, 4CAI

PubMed Abstract:
Mutations in dysferlin, the first protein linked with the cell membrane repair mechanism, causes a group of muscular dystrophies called dysferlinopathies. Dysferlin is a type two-anchored membrane protein, with a single C terminal trans-membrane helix, and most of the protein lying in cytoplasm. Dysferlin contains several C2 domains and two DysF domains which are nested one inside the other. Many pathogenic point mutations fall in the DysF domain region.

Organizational Affiliation

Crystallography, Biological Sciences, Institute for Structural and Molecular Biology, Birkbeck University of London, Malet Street, London WC1E 7HX, UK. n.keep@mail.cryst.bbk.ac.uk.

Macromolecule Content

Total Structure Weight: 13.89 kDa
Atom Count: 1,039
Modelled Residue Count: 109
Deposited Residue Count: 112
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DYSFERLIN	A [auth B]	112	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O75923 (Homo sapiens) Explore O75923 Go to UniProtKB: O75923
PHAROS: O75923 GTEx: ENSG00000135636
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75923
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain B MOL2 format, chain D [auth B] MOL2 format, chain C [auth B]	B, C [auth B], D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain B Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.191
R-Value Work: 0.177
R-Value Observed: 0.178
Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.953	α = 90
b = 75.953	β = 90
c = 75.953	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MrBUMP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-01-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-01-29
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description