SAXSdb — 4nkn

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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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 2–117 Chain B； UniProt 2–117 Chain E； UniProt 2–117	Fragment：N-terminal domain (UNP residues 1-116) Mutation：L67M, I101M Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 2–117 Chain D； UniProt 2–117 Chain F； UniProt 2–117	Fragment：N-terminal domain (UNP residues 1-116) Mutation：L67M, I101M Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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

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 4NKN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4OE9 The crystal structure of the n-terminal domain of COMMD9 Deposited 2014-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–117（117 aa） 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
4OE9 The crystal structure of the n-terminal domain of COMMD9 Deposited 2014-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–117（117 aa） 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
6BP6 Crystal structure of Commd9 COMM domain Deposited 2017-11-22	Different construct Different mutation/modification Different oligomeric state 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 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 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 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 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 6–121； UniProt 2–117 Author chain B； PDBConstruct 6–121； UniProt 2–117 Author chain C； PDBConstruct 6–121； UniProt 2–117 Author chain D； PDBConstruct 6–121； UniProt 2–117 Author chain E； PDBConstruct 6–121； UniProt 2–117 Author chain F； PDBConstruct 6–121； UniProt 2–117

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	4nkn
Deposition date deposition_date	2013-11-12
Structure title title	The Crystal Structure of the N-terminal domain of COMMD9
Keywords keywords	Domain-swapped Trimer, All helical protein, 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	35.20 Å
Radius of gyration Rg (electron density) rg_electron	35.16 Å
Forward intensity I(0) i0	78160300.00
Molecular weight molecular_weight	70020.0 kDa
Excluded volume excluded_volume	87460 Å³
Envelope volume envelope_volume	123160 Å³
Hydration-shell volume shell_volume	31709 Å³
Envelope diameter envelope_diameter	116.4 Å
Shell Rg shell_rg	38.24 Å
Envelope Rg envelope_rg	34.90 Å
Shape Rg shape_rg	35.19 Å
Total Rg total_rg	35.34 Å
Total atoms total_atoms	4880
Residues n_residues	651
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	118.0 Å
Rg (real space) rg_real	35.46 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	7.8160e+07
I(0) uncertainty (real space) i0_real_error	1.2860e+06
Rg (reciprocal space) rg_reciprocal	35.30 Å
I(0) (reciprocal space) i0_reciprocal	78150000.0000
Solution quality estimate total_estimate	0.8506
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.1 Å
Skewness Skewness skewness	0.435
Kurtosis Kurtosis kurtosis	-0.614
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6901000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.776; Smooth: 0.894

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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	89.690 Å
Unit-cell length b length_b	79.757 Å
Unit-cell length c length_c	131.164 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.790 Å
Low-resolution limit resolution_low	32.789 Å
R factor r_factor	0.2117
R_work r_work	0.2097
R_free r_free	0.2495

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	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	4971

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

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	91

fit	/app/data/saxs_computation/nk/4nkn/4nkn.fit
pddf	/app/data/pr_computation/nk/4nkn/4nkn.pr.out
profile	/app/data/saxs_computation/nk/4nkn/4nkn.dat