SAXSdb — 9ec1

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dystrophin

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2933–3046	Fragment：spectrin repeat 24	SO4 SULFATE ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2933–3046	Fragment：spectrin repeat 24	SO4 SULFATE ION × 2 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 2933–3046	Fragment：spectrin repeat 24	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 2933–3046	Fragment：spectrin repeat 24	SO4 SULFATE ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 2933–3046	Fragment：spectrin repeat 24	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 2933–3046	Fragment：spectrin repeat 24	SO4 SULFATE ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 2933–3046	Fragment：spectrin repeat 24	SO4 SULFATE ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 2933–3046	Fragment：spectrin repeat 24	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9EC1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DXX N-terminal Actin-binding Domain of Human Dystrophin Deposited 2000-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa） Fragment：ACTIN-BINDING Chain B 1–246（246 aa） Fragment：ACTIN-BINDING	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；1.55M AMMONIUM FORMATE, 0.1M HEPES 7.4, pH 7.40	Resolution 2.60 Å R-free 0.268
1DXX N-terminal Actin-binding Domain of Human Dystrophin Deposited 2000-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–246（246 aa） Fragment：ACTIN-BINDING Chain D 1–246（246 aa） Fragment：ACTIN-BINDING	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；1.55M AMMONIUM FORMATE, 0.1M HEPES 7.4, pH 7.40	Resolution 2.60 Å R-free 0.268
1EG3 STRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX WITH A BETA-DYSTROGLYCAN PEPTIDE Deposited 2000-02-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3046–3306（261 aa） Fragment：WW DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；ammonium sulfate, glycerol, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.257
1EG4 STRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX WITH A BETA-DYSTROGLYCAN PEPTIDE Deposited 2000-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 3046–3306（261 aa） Fragment：WW DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；ammonium sulfate, glycerol, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.249
3UUN Crystal Structure of N-terminal first spectrin repeat of dystrophin Deposited 2011-11-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 338–456（119 aa） Fragment：Spectrin Repeat, UNP residues 338-456	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294.15 K；0.1M Tris HCl, 2.0M Ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K	Resolution 2.30 Å R-free 0.260
3UUN Crystal Structure of N-terminal first spectrin repeat of dystrophin Deposited 2011-11-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 338–456（119 aa） Fragment：Spectrin Repeat, UNP residues 338-456	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294.15 K；0.1M Tris HCl, 2.0M Ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K	Resolution 2.30 Å R-free 0.260
3UUN Crystal Structure of N-terminal first spectrin repeat of dystrophin Deposited 2011-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 338–456（119 aa） Fragment：Spectrin Repeat, UNP residues 338-456 Chain B 338–456（119 aa） Fragment：Spectrin Repeat, UNP residues 338-456	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294.15 K；0.1M Tris HCl, 2.0M Ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K	Resolution 2.30 Å R-free 0.260
9D58 Human Dystrophin tandem calponin homology actin-binding domain crystallized in a closed-state conformation Deposited 2024-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–246（245 aa） Fragment：actin-binding domain/calponin homology domains 1 and 2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.7, 30% w/v Polyethylene monomethyl ether (MPEG) 5,000	Resolution 1.94 Å R-free 0.262
9D58 Human Dystrophin tandem calponin homology actin-binding domain crystallized in a closed-state conformation Deposited 2024-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–246（245 aa） Fragment：actin-binding domain/calponin homology domains 1 and 2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.7, 30% w/v Polyethylene monomethyl ether (MPEG) 5,000	Resolution 1.94 Å R-free 0.262
9D58 Human Dystrophin tandem calponin homology actin-binding domain crystallized in a closed-state conformation Deposited 2024-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–246（245 aa） Fragment：actin-binding domain/calponin homology domains 1 and 2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.7, 30% w/v Polyethylene monomethyl ether (MPEG) 5,000	Resolution 1.94 Å R-free 0.262
9D58 Human Dystrophin tandem calponin homology actin-binding domain crystallized in a closed-state conformation Deposited 2024-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2–246（245 aa） Fragment：actin-binding domain/calponin homology domains 1 and 2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.7, 30% w/v Polyethylene monomethyl ether (MPEG) 5,000	Resolution 1.94 Å R-free 0.262

5 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DMD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–117； UniProt 2933–3046 Author chain B； PDBConstruct 4–117； UniProt 2933–3046 Author chain C； PDBConstruct 4–117； UniProt 2933–3046 Author chain D； PDBConstruct 4–117； UniProt 2933–3046 Author chain E； PDBConstruct 4–117； UniProt 2933–3046 Author chain F； PDBConstruct 4–117； UniProt 2933–3046 Author chain G； PDBConstruct 4–117； UniProt 2933–3046 Author chain H； PDBConstruct 4–117； UniProt 2933–3046

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ec1
Deposition date deposition_date	2024-11-13
Structure title title	The Structure of Human Dystrophin Spectrin Repeat 24
Keywords keywords	Spectrin Repeat, Spectrin, Dystrophin, Duchenne Muscular Dystrophy, DMD, Cytoskeleton, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.44 Å
Radius of gyration Rg (electron density) rg_electron	36.00 Å
Forward intensity I(0) i0	191270000.00
Molecular weight molecular_weight	107250.0 kDa
Excluded volume excluded_volume	133060 Å³
Envelope volume envelope_volume	186180 Å³
Hydration-shell volume shell_volume	44100 Å³
Envelope diameter envelope_diameter	133.3 Å
Shell Rg shell_rg	41.07 Å
Envelope Rg envelope_rg	35.36 Å
Shape Rg shape_rg	36.00 Å
Total Rg total_rg	36.38 Å
Total atoms total_atoms	7530
Residues n_residues	929
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	129.7 Å
Rg (real space) rg_real	36.52 Å
Rg uncertainty (real space) rg_real_error	1.29 Å
I(0) (real space) i0_real	1.9130e+08
I(0) uncertainty (real space) i0_real_error	3.5290e+06
Rg (reciprocal space) rg_reciprocal	36.47 Å
I(0) (reciprocal space) i0_reciprocal	191300000.0000
Solution quality estimate total_estimate	0.8594
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.2 Å
Skewness Skewness skewness	0.401
Kurtosis Kurtosis kurtosis	-0.294
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24480000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.901; Smooth: 0.979

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Dystrophin
Molecular weight formula_weight	13347.0 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	7630

STGLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

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8. Citations (1)

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Unit-cell length a length_a	106.003 Å
Unit-cell length b length_b	106.003 Å
Unit-cell length c length_c	614.847 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	96

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	hexagonal

Resolution resolution	2.140 Å
Low-resolution limit resolution_low	34.480 Å
R factor r_factor	0.2187
R_work r_work	0.2168
R_free r_free	0.2545

fit	/app/data/saxs_computation/ec/9ec1/9ec1.fit
pddf	/app/data/pr_computation/ec/9ec1/9ec1.pr.out
profile	/app/data/saxs_computation/ec/9ec1/9ec1.dat

The Structure of Human Dystrophin Spectrin Repeat 24

1. Protein Identity and Related Structures Protein Identity & Related Structures

Dystrophin

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction