SAXSdb — 9zmy

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

COMM domain-containing protein 10

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 12–127 Chain B； UniProt 12–127	Fragment：HN domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；293 K；30% PEG400 in 0.1 M Tris pH 8.0	Resolution 1.62 Å R-free 0.241

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 9ZMY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8ESD Crystal structure of COMMD7-COMMD9-COMMD5-COMMD10 tetramer Deposited 2022-10-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain T 12–202（191 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；2 uM crown ether and 10% glycerol and grown in 22% ethanol and 5 mM EDTA	Resolution 3.33 Å R-free 0.278
8F2R Human CCC complex Deposited 2022-11-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain J 5–202（198 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2；50 mM HEPES pH7.2, 150 mM NaCl, 2mM beta-mercaptoethanol, 0.01% Triton-X100 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å
8F2U Human CCC complex Deposited 2022-11-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain J 1–202（202 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2；50 mM HEPES pH7.2, 150 mM NaCl, 2mM beta-mercaptoethanol, 0.01% Triton-X100 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.53 Å
8P0W Structure of the human Commander complex COMMD ring Deposited 2023-05-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain J 1–202（202 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9ZN0 Crystal structure of the Commd10 S50E HN domain mutant in domain swapped conformation Deposited 2025-12-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 12–127（116 aa） Chain C 12–127（116 aa）	Not recorded	LEA PENTANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；0.1 M Tris (pH 8.5), 0.1 M Mg formate, and 30% PE14/4, with 10% glycerol used as cryoprotectant	Resolution 2.12 Å R-free 0.243
9ZN0 Crystal structure of the Commd10 S50E HN domain mutant in domain swapped conformation Deposited 2025-12-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 12–127（116 aa） Chain D 12–127（116 aa）	Not recorded	LEA PENTANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；0.1 M Tris (pH 8.5), 0.1 M Mg formate, and 30% PE14/4, with 10% glycerol used as cryoprotectant	Resolution 2.12 Å R-free 0.243

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COMDA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–116； UniProt 12–127 Author chain B； PDBConstruct 1–116； UniProt 12–127

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	9zmy
Deposition date deposition_date	2025-12-11
最后修订 last_revision	2026-01-21
Structure title title	Crystal structure of the human Commd10 HN domain in domain swapped conformation
Keywords keywords	COMMD, Commander, endosome, EXOCYTOSIS; EXOCYTOSIS
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	30.91 Å
Radius of gyration Rg (electron density) rg_electron	32.00 Å
Forward intensity I(0) i0	11415500.00
Molecular weight molecular_weight	25991.0 kDa
Excluded volume excluded_volume	32773 Å³
Envelope volume envelope_volume	54710 Å³
Hydration-shell volume shell_volume	17048 Å³
Envelope diameter envelope_diameter	121.5 Å
Shell Rg shell_rg	31.55 Å
Envelope Rg envelope_rg	32.91 Å
Shape Rg shape_rg	31.89 Å
Total Rg total_rg	32.31 Å
Total atoms total_atoms	1833
Residues n_residues	227
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	118.7 Å
Rg (real space) rg_real	31.68 Å
Rg uncertainty (real space) rg_real_error	1.66 Å
I(0) (real space) i0_real	1.1420e+07
I(0) uncertainty (real space) i0_real_error	1.9510e+05
Rg (reciprocal space) rg_reciprocal	31.34 Å
I(0) (reciprocal space) i0_reciprocal	11410000.0000
Solution quality estimate total_estimate	0.7243
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.3 Å
Skewness Skewness skewness	0.839
Kurtosis Kurtosis kurtosis	0.550
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	699400.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.474; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.279; Smooth: 0.710

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	41.624 Å
Unit-cell length b length_b	59.852 Å
Unit-cell length c length_c	96.847 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.619 Å
Low-resolution limit resolution_low	34.173 Å
R factor r_factor	0.2131
R_work r_work	0.2111
R_free r_free	0.2411

Description description	COMM domain-containing protein 10
Molecular weight formula_weight	13396.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1926

Crystal structure of the human Commd10 HN domain in domain swapped conformation

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

COMM domain-containing protein 10

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

fit	/app/data/saxs_computation/zm/9zmy/9zmy.fit
pddf	/app/data/pr_computation/zm/9zmy/9zmy.pr.out
profile	/app/data/saxs_computation/zm/9zmy/9zmy.dat