SAXSdb — 9zd5

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

Stomatin

OrganismNot specified

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 25–200 Chain G； UniProt 25–200 Chain H； UniProt 25–200 Chain I； UniProt 25–200	Not recorded	PLM PALMITIC ACID × 12 PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 4 S1P (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.20 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.

Other PDB	Difference from Current Entry 9ZD5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7WH3 Solution structure of human stomatin SPFH domain in a phosphate buffer Deposited 2021-12-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 94–202（109 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 200；Pressure 1 NMR sample composition 100 uM [U-100% 15N] SPFH domain from stomatin, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 600 uM [U-100% 13C; U-100% 15N] SPFH domain from stomatin, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 600 uM [U-100% 13C] SPFH domain from stomatin, 100% D2O \| 100% D2O	Resolution not provided
9OH9 Human Stomatin Complex in Native Membrane Vesicles Deposited 2025-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion	Assembly 1 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: 16-meric	Chain A 2–288（287 aa） Chain B 2–288（287 aa） Chain C 2–288（287 aa） Chain D 2–288（287 aa） Chain E 2–288（287 aa） Chain F 2–288（287 aa） Chain G 2–288（287 aa） Chain H 2–288（287 aa） Chain I 2–288（287 aa） Chain J 2–288（287 aa） Chain K 2–288（287 aa） Chain L 2–288（287 aa） Chain M 2–288（287 aa） Chain N 2–288（287 aa） Chain O 2–288（287 aa） Chain P 2–288（287 aa）	Not recorded	NA SODIUM ION × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.20 Å
9Z7U Human Stomatin - C8 Symmetry Deposited 2025-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric	Chain B 25–280（256 aa） Chain C 25–280（256 aa） Chain E 25–280（256 aa） Chain F 25–280（256 aa） Chain G 25–280（256 aa） Chain H 25–280（256 aa） Chain J 25–280（256 aa） Chain K 25–280（256 aa） Chain M 25–280（256 aa） Chain N 25–280（256 aa） Chain P 25–280（256 aa） Chain Q 25–280（256 aa） Chain S 25–280（256 aa） Chain T 25–280（256 aa） Chain V 25–280（256 aa） Chain W 25–280（256 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.00 Å
9ZD2 C1 local refinement of aquaporin 1 bound to endogenous human stomatin Deposited 2025-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain E 25–200（176 aa） Chain F 25–200（176 aa） Chain G 25–200（176 aa） Chain H 25–200（176 aa） Chain I 25–200（176 aa）	Not recorded	PLM PALMITIC ACID × 4 CLR CHOLESTEROL × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STOM_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 19–194； UniProt 25–200 Author chain G； PDBConstruct 19–194； UniProt 25–200 Author chain H； PDBConstruct 19–194； UniProt 25–200 Author chain I； PDBConstruct 19–194； UniProt 25–200

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	9zd5
Deposition date deposition_date	2025-11-24
Structure title title	Human Stomatin - intramembrane region
Keywords keywords	Oligomer, C8 symmetry, scaffold, MEMBRANE PROTEIN, intramembrane region; MEMBRANE PROTEIN
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	32.98 Å
Radius of gyration Rg (electron density) rg_electron	33.75 Å
Forward intensity I(0) i0	103468000.00
Molecular weight molecular_weight	90171.0 kDa
Excluded volume excluded_volume	116960 Å³
Envelope volume envelope_volume	154930 Å³
Hydration-shell volume shell_volume	37926 Å³
Envelope diameter envelope_diameter	120.6 Å
Shell Rg shell_rg	40.58 Å
Envelope Rg envelope_rg	33.82 Å
Shape Rg shape_rg	33.72 Å
Total Rg total_rg	34.50 Å
Total atoms total_atoms	6340
Residues n_residues	776
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	105.4 Å
Rg (real space) rg_real	33.04 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	1.0350e+08
I(0) uncertainty (real space) i0_real_error	1.5400e+06
Rg (reciprocal space) rg_reciprocal	33.02 Å
I(0) (reciprocal space) i0_reciprocal	103500000.0000
Solution quality estimate total_estimate	0.8972
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.3 Å
Skewness Skewness skewness	0.311
Kurtosis Kurtosis kurtosis	-0.484
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22380000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.857

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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	Stomatin
Molecular weight formula_weight	21128.7 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,E,G,H
Atom count atom_count	6340

XXXXXXXXXXXXXXXXXXKGLGPCGWILVAFSFLFTVITFPISIWMCIKIIKEYERAIIFRLGRILQGGAKGPGLFFILPCTDSFIKVDMRTISFDIPPQEILTKDSVTISVDGVVYYRVQNATLAVANITNADSATRLLAQTTLRNVLGTKNLSQILSDREEIAHNMQSTLDDATDAWGIKVERVEIKDVKLP

Entity 2 Entity 2 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	nat
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	DIUNDECYL PHOSPHATIDYL CHOLINE
Molecular weight formula_weight	622.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
Molecular weight formula_weight	379.5 kDa
Source method src_method	syn
Copy count entity_count	4

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	2.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	2151648

fit	/app/data/saxs_computation/zd/9zd5/9zd5.fit
pddf	/app/data/pr_computation/zd/9zd5/9zd5.pr.out
profile	/app/data/saxs_computation/zd/9zd5/9zd5.dat

Human Stomatin - intramembrane region

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

Stomatin

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

冷冻电镜 EM 3D