9EC1 | pdb_00009ec1

The Structure of Human Dystrophin Spectrin Repeat 24

PDB DOI: https://doi.org/10.2210/pdb9EC1/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-11-13 Released: 2026-04-22
Deposition Author(s): Streeter, O., Shi, K., Bui, H.N., Ervasti, J.M., Evans III, R.L., Muretta, J.M.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.255 (Depositor), 0.255 (DCC)
R-Value Work:
0.217 (Depositor), 0.215 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

The atomic structure of human dystrophin spectrin-like repeat 24.

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

(2026) Acta Crystallogr F Struct Biol Commun 82: 184-193

PubMed: 42024151 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X26003262
Primary Citation Related Structures:
9EC1

PubMed Abstract:
The structure of spectrin-like repeat 24 of human dystrophin was determined at 2.5 Å effective resolution. The structure exhibits a three-helix bundle fold, common to all spectrin-repeat family members, and shares a high degree of homology with existing structures of spectrin-like repeat 1 from dystrophin and utrophin. The structure provides molecular details of the atomic interactions that stabilize the repeat, including hydrophobic interactions and inter-helix and intra-helix salt bridges. AlphaFold models of the repeat are in excellent agreement with the structure, showing an all-atom r.m.s.d. of 1.13 Å. Accurate modeling of SR24 supports AlphaFold modeling of all 24 of the dystrophin spectrin-like repeats and the use of these models in predicting the molecular determinants of dystrophin stability, a key aspect of its biological function as a structural protein that cross-links actin filaments to the dystrophin-glycoprotein complex to mediate a mechanical connection between the cytoskeleton and the extracellular matrix.

Organizational Affiliation

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, 6-155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA.

Macromolecule Content

Total Structure Weight: 108.38 kDa
Atom Count: 7,630
Modeled Residue Count: 929
Deposited Residue Count: 936
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dystrophin	A, B, C, D, E A, B, C, D, E, F, G, H	117	Homo sapiens	Mutation(s): 1 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11532
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain V [auth E] SDF format, chain S [auth D] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain CA [auth G] SDF format, chain BA [auth G] SDF format, chain AA [auth G] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain V [auth E] MOL2 format, chain S [auth D] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth G] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain V [auth E] mmCIF format, chain S [auth D] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth G]	AA [auth G] BA [auth G] CA [auth G] I [auth A] J [auth A] AA [auth G], BA [auth G], CA [auth G], I [auth A], J [auth A], M [auth B], N [auth B], R [auth C], S [auth D], V [auth E], W [auth F], X [auth F], Z [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Z [auth G]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain EA [auth H] SDF format, chain DA [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain EA [auth H] MOL2 format, chain DA [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain EA [auth H] mmCIF format, chain DA [auth G]	DA [auth G] EA [auth H] K [auth A] L [auth A] O [auth B] DA [auth G], EA [auth H], K [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], T [auth D], U [auth D], Y [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth G] Focus chain EA [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth D] Focus chain U [auth D] Focus chain Y [auth F] Interactions & Density Focus chain DA [auth G] Focus chain EA [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth D] Focus chain U [auth D] Focus chain Y [auth F]