SAXSdb — 9zn0

▼

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 C； UniProt 12–127	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 12–127 Chain D； UniProt 12–127	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

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 9ZN0	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
9ZMY Crystal structure of the human Commd10 HN domain 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） Fragment：HN domain Chain B 12–127（116 aa） Fragment：HN domain	Not recorded	No recorded non-water small molecule	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

5 other PDB entries and 5 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 6–121； UniProt 12–127 Author chain B； PDBConstruct 6–121； UniProt 12–127 Author chain C； PDBConstruct 6–121； UniProt 12–127 Author chain D； PDBConstruct 6–121； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9zn0
Deposition date deposition_date	2025-12-11
最后修订 last_revision	2026-01-21
Structure title title	Crystal structure of the Commd10 S50E HN domain mutant in domain swapped conformation
Keywords keywords	Commander, COMMD, endosome, EXOCYTOSIS; EXOCYTOSIS
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	26.81 Å
Radius of gyration Rg (electron density) rg_electron	26.04 Å
Forward intensity I(0) i0	45661500.00
Molecular weight molecular_weight	52968.0 kDa
Excluded volume excluded_volume	66768 Å³
Envelope volume envelope_volume	84700 Å³
Hydration-shell volume shell_volume	28320 Å³
Envelope diameter envelope_diameter	92.7 Å
Shell Rg shell_rg	32.03 Å
Envelope Rg envelope_rg	25.80 Å
Shape Rg shape_rg	26.02 Å
Total Rg total_rg	26.79 Å
Total atoms total_atoms	7512
Residues n_residues	462
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

▼

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

Maximum dimension Dmax dmax	90.1 Å
Rg (real space) rg_real	26.83 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	4.5660e+07
I(0) uncertainty (real space) i0_real_error	6.9650e+05
Rg (reciprocal space) rg_reciprocal	26.82 Å
I(0) (reciprocal space) i0_reciprocal	45660000.0000
Solution quality estimate total_estimate	0.8663
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.1 Å
Skewness Skewness skewness	0.416
Kurtosis Kurtosis kurtosis	-0.089
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11900000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.812

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	COMM domain-containing protein 10
Molecular weight formula_weight	13849.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7887

GPLGSSPSMKKAVSLINAIDTGRFPRLLTRILQKLHLKAESSFEEEEEEKLQAAFSLEKQDLHLVLETISFILEQAVYHNVKPAALQQQLENIHLRQDKAEAFVNTWSSMGQETVEKFRQR

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	PENTANOIC ACID
Molecular weight formula_weight	102.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	125

▶

8. Citations (1)

▶

Unit-cell length a length_a	43.759 Å
Unit-cell length b length_b	92.173 Å
Unit-cell length c length_c	59.815 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.120 Å
Low-resolution limit resolution_low	40.760 Å
R factor r_factor	0.1943
R_work r_work	0.1897
R_free r_free	0.2433

fit	/app/data/saxs_computation/zn/9zn0/9zn0.fit
pddf	/app/data/pr_computation/zn/9zn0/9zn0.pr.out
profile	/app/data/saxs_computation/zn/9zn0/9zn0.dat

Crystal structure of the Commd10 S50E HN domain mutant 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