← Back to search
9zmz

Crystal structure of the human Commd4 HN domain in a domain swapped conformation

Method: X-RAY DIFFRACTION Dmax: 54.0 Å Quality: EXCELLENT
▼

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

COMM domain-containing protein 4

Homo sapiens

UniProt Q9H0A8

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 12–122 Fragment：HN domain No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；293 K；0.1 M Tris (pH 8.0) and 28% PEG4000 Resolution 2.12 Å R-free 0.304

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 9ZMZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8F2R Human CCC complex Deposited 2022-11-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain D 1–199（199 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–199（199 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–199（199 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

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COMD4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–112； UniProt 12–122

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9zmz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9zmz
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9zmz
Deposition date deposition_date2025-12-11
最后修订 last_revision2026-01-21
Structure title titleCrystal structure of the human Commd4 HN domain in a domain swapped conformation
Keywords keywordsCOMMD, endosome, Commander, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier17.59 Å
Radius of gyration Rg (electron density) rg_electron16.41 Å
Forward intensity I(0) i02274240.00
Molecular weight molecular_weight10723.0 kDa
Excluded volume excluded_volume13613 ų
Envelope volume envelope_volume18574 ų
Hydration-shell volume shell_volume10380 ų
Envelope diameter envelope_diameter52.8 Å
Shell Rg shell_rg20.71 Å
Envelope Rg envelope_rg15.98 Å
Shape Rg shape_rg16.37 Å
Total Rg total_rg17.49 Å
Total atoms total_atoms1533
Residues n_residues99
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax54.0 Å
Rg (real space) rg_real17.50 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real2.2740e+06
I(0) uncertainty (real space) i0_real_error2.5700e+04
Rg (reciprocal space) rg_reciprocal17.51 Å
I(0) (reciprocal space) i0_reciprocal2274000.0000
Solution quality estimate total_estimate0.9031
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary19.4 Å
Skewness Skewness skewness-0.028
Kurtosis Kurtosis kurtosis-0.624
Angular range angular_range— – 0.4500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha105300.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.975
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

9. Files and Curves (10)