9za1

cryoEM structure of COMMD-like protein S4Y171 octamer

Method: ELECTRON MICROSCOPY D_max: 136.8 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 1–210 Chain B； UniProt 1–210 Chain C； UniProt 1–210 Chain D； UniProt 1–210 Chain E； UniProt 1–210 Chain G； UniProt 1–210 Chain H； UniProt 1–210 Chain N； UniProt 1–210	Not recorded	No other associated polymer	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 3.40 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	S4Y171_SORCE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–216； UniProt 1–210 Author chain B； PDBConstruct 7–216； UniProt 1–210 Author chain C； PDBConstruct 7–216； UniProt 1–210 Author chain D； PDBConstruct 7–216； UniProt 1–210 Author chain E； PDBConstruct 7–216； UniProt 1–210 Author chain G； PDBConstruct 7–216； UniProt 1–210 Author chain H； PDBConstruct 7–216； UniProt 1–210 Author chain N； PDBConstruct 7–216； UniProt 1–210

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	9za1
Deposition date deposition_date	2025-11-18
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	43.44 Å
Radius of gyration Rg (electron density) rg_electron	42.69 Å
Forward intensity I(0) i0	438717000.00
Molecular weight molecular_weight	170120.0 kDa
Excluded volume excluded_volume	213470 Å³
Envelope volume envelope_volume	336540 Å³
Hydration-shell volume shell_volume	66652 Å³
Envelope diameter envelope_diameter	133.6 Å
Shell Rg shell_rg	47.39 Å
Envelope Rg envelope_rg	41.28 Å
Shape Rg shape_rg	42.71 Å
Total Rg total_rg	42.90 Å
Total atoms total_atoms	24352
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	136.8 Å
Rg (real space) rg_real	43.18 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	4.3870e+08
I(0) uncertainty (real space) i0_real_error	7.7190e+06
Rg (reciprocal space) rg_reciprocal	43.44 Å
I(0) (reciprocal space) i0_reciprocal	438800000.0000
Solution quality estimate total_estimate	0.7939
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	57.0 Å
Skewness Skewness skewness	0.086
Kurtosis Kurtosis kurtosis	-0.348
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30740000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.000

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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	3.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	73912

Description description	COMM domain-containing protein
Molecular weight formula_weight	27920.1 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,G,H,N
Atom count atom_count	24352

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/9za1/9za1.fit
pddf	/app/data/pr_computation/za/9za1/9za1.pr.out
profile	/app/data/saxs_computation/za/9za1/9za1.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)