SAXSdb — 4oe9

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

COMM domain-containing protein 9

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 1–117	Fragment：COMMD9, unp residues 1-117 Mutation：L67M, I101M Non-standard monomer：Yes (specific site not provided by mmCIF)	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.9；291.15 K；28% mPEG 5000, 0.2M citric acid, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 1.55 Å R-free 0.165
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–117	Fragment：COMMD9, unp residues 1-117 Mutation：L67M, I101M Non-standard monomer：Yes (specific site not provided by mmCIF)	CIT CITRIC ACID × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.9；291.15 K；28% mPEG 5000, 0.2M citric acid, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 1.55 Å R-free 0.165

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 4OE9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NKN The Crystal Structure of the N-terminal domain of COMMD9 Deposited 2013-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–117（116 aa） Fragment：N-terminal domain (UNP residues 1-116) Chain B 2–117（116 aa） Fragment：N-terminal domain (UNP residues 1-116) Chain E 2–117（116 aa） Fragment：N-terminal domain (UNP residues 1-116)	Mutation：L67M, I101M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L67M, I101M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L67M, I101M Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291.15 K；20% PEG 3350, 0.2M Mg Nitrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.79 Å R-free 0.249
4NKN The Crystal Structure of the N-terminal domain of COMMD9 Deposited 2013-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain C 2–117（116 aa） Fragment：N-terminal domain (UNP residues 1-116) Chain D 2–117（116 aa） Fragment：N-terminal domain (UNP residues 1-116) Chain F 2–117（116 aa） Fragment：N-terminal domain (UNP residues 1-116)	Mutation：L67M, I101M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L67M, I101M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L67M, I101M Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291.15 K；20% PEG 3350, 0.2M Mg Nitrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.79 Å R-free 0.249
6BP6 Crystal structure of Commd9 COMM domain Deposited 2017-11-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 115–198（84 aa） Chain B 115–198（84 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M HEPES (pH 7.0), 6% Jeffamine M-600	Resolution 2.17 Å R-free 0.285
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 N 5–198（194 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 I 1–198（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 I 1–198（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 3.53 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 I 1–198（198 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

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COMD9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–121； UniProt 1–117 Author chain B； PDBConstruct 5–121； UniProt 1–117

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	4oe9
Deposition date deposition_date	2014-01-12
Structure title title	The crystal structure of the n-terminal domain of COMMD9
Keywords keywords	ALL ALPHA HELICAL, PROTEIN BINDING; PROTEIN BINDING
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	20.07 Å
Radius of gyration Rg (electron density) rg_electron	18.99 Å
Forward intensity I(0) i0	12759500.00
Molecular weight molecular_weight	26331.0 kDa
Excluded volume excluded_volume	32744 Å³
Envelope volume envelope_volume	38134 Å³
Hydration-shell volume shell_volume	17397 Å³
Envelope diameter envelope_diameter	71.7 Å
Shell Rg shell_rg	24.66 Å
Envelope Rg envelope_rg	19.34 Å
Shape Rg shape_rg	19.00 Å
Total Rg total_rg	19.80 Å
Total atoms total_atoms	3618
Residues n_residues	229
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	73.9 Å
Rg (real space) rg_real	20.12 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	1.2760e+07
I(0) uncertainty (real space) i0_real_error	1.8590e+05
Rg (reciprocal space) rg_reciprocal	20.11 Å
I(0) (reciprocal space) i0_reciprocal	12760000.0000
Solution quality estimate total_estimate	0.8278
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.448
Kurtosis Kurtosis kurtosis	-0.217
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4041000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.631; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.865; Smooth: 1.000

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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	COMM domain-containing protein 9
Molecular weight formula_weight	13562.9 kDa
Mutation mutation	L67M, I101M
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3941

MSGAMAALTAEHFAALQSLLKASSKDVVRQLCQESFSSSALGLKKLLDVTCSSLSVTQEEAEELLQALHRMTRLVAFRDLSSAEAILALFPENFHQNLKNLLTKIMLEHVSTWRTEAQANQ

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	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	254

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8. Citations (1)

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Unit-cell length a length_a	28.490 Å
Unit-cell length b length_b	35.580 Å
Unit-cell length c length_c	54.300 Å
Unit-cell angle α angle_alpha	104.03 °
Unit-cell angle β angle_beta	93.30 °
Unit-cell angle γ angle_gamma	91.11 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	26.286 Å
R factor r_factor	0.1355
R_work r_work	0.1339
R_free r_free	0.1651

fit	/app/data/saxs_computation/oe/4oe9/4oe9.fit
pddf	/app/data/pr_computation/oe/4oe9/4oe9.pr.out
profile	/app/data/saxs_computation/oe/4oe9/4oe9.dat

The crystal structure of the n-terminal domain of COMMD9

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

COMM domain-containing protein 9

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