9za2

cryoEM structure of COMMD-like protein S4Y171 octamer

Method: ELECTRON MICROSCOPY D_max: 132.0 Å Quality: GOOD

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

COMM domain-containing protein

Sorangium cellulosum So0157-2

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–226 Chain B； UniProt 1–226 Chain C； UniProt 1–226 Chain D； UniProt 1–226 Chain E； UniProt 1–226 Chain F； UniProt 1–226 Chain G； UniProt 1–226 Chain H； UniProt 1–226	Not recorded	No other associated polymer	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 4.70 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	S4XVP2_SORCE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–232； UniProt 1–226 Author chain B； PDBConstruct 7–232； UniProt 1–226 Author chain C； PDBConstruct 7–232； UniProt 1–226 Author chain D； PDBConstruct 7–232； UniProt 1–226 Author chain E； PDBConstruct 7–232； UniProt 1–226 Author chain F； PDBConstruct 7–232； UniProt 1–226 Author chain G； PDBConstruct 7–232； UniProt 1–226 Author chain H； PDBConstruct 7–232； UniProt 1–226

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9za2
Deposition date deposition_date	2025-11-19
Structure title title	cryoEM structure of COMMD-like protein S4Y171 octamer
Keywords keywords	Commd-like, octamer, bacterial, Commd, Commander, UNKNOWN FUNCTION; UNKNOWN FUNCTION
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	42.56 Å
Radius of gyration Rg (electron density) rg_electron	41.93 Å
Forward intensity I(0) i0	469068000.00
Molecular weight molecular_weight	173190.0 kDa
Excluded volume excluded_volume	216190 Å³
Envelope volume envelope_volume	348390 Å³
Hydration-shell volume shell_volume	69914 Å³
Envelope diameter envelope_diameter	129.6 Å
Shell Rg shell_rg	47.39 Å
Envelope Rg envelope_rg	40.06 Å
Shape Rg shape_rg	41.94 Å
Total Rg total_rg	42.21 Å
Total atoms total_atoms	24552
Residues n_residues	1584
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	132.0 Å
Rg (real space) rg_real	42.29 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	4.6910e+08
I(0) uncertainty (real space) i0_real_error	7.7390e+06
Rg (reciprocal space) rg_reciprocal	42.56 Å
I(0) (reciprocal space) i0_reciprocal	469200000.0000
Solution quality estimate total_estimate	0.8736
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	57.1 Å
Skewness Skewness skewness	0.057
Kurtosis Kurtosis kurtosis	-0.384
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	45390000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.919

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Resolution resolution	4.70 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	28401

Description description	COMM domain-containing protein
Molecular weight formula_weight	29816.2 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	24552

来源生物 organism	Sorangium cellulosum So0157-2
NCBI Class编号 ncbi_taxonomy_id	1254432
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/za/9za2/9za2.fit
pddf	/app/data/pr_computation/za/9za2/9za2.pr.out
profile	/app/data/saxs_computation/za/9za2/9za2.dat

cryoEM structure of COMMD-like protein S4Y171 octamer

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

COMM domain-containing protein

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)