← Back to search
9z7u

Human Stomatin - C8 Symmetry

Method: ELECTRON MICROSCOPY Dmax: 153.4 Å Quality: GOOD
▼

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

Stomatin

OrganismNot specified

UniProt P27105

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 × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain B； UniProt 25–280 Chain C； UniProt 25–280 Chain E； UniProt 25–280 Chain F； UniProt 25–280 Chain G； UniProt 25–280 Chain H； UniProt 25–280 Chain J； UniProt 25–280 Chain K； UniProt 25–280 Chain M； UniProt 25–280 Chain N； UniProt 25–280 Chain P； UniProt 25–280 Chain Q； UniProt 25–280 Chain S； UniProt 25–280 Chain T； UniProt 25–280 Chain V； UniProt 25–280 Chain W； UniProt 25–280 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.00 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 9Z7U 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 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 ligand/ion Different structure-quality metrics 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
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
9ZD5 Human Stomatin - intramembrane region Deposited 2025-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 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 × 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

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 B； PDBConstruct 19–274； UniProt 25–280 Author chain C； PDBConstruct 19–274； UniProt 25–280 Author chain E； PDBConstruct 19–274； UniProt 25–280 Author chain F； PDBConstruct 19–274； UniProt 25–280 Author chain G； PDBConstruct 19–274； UniProt 25–280 Author chain H； PDBConstruct 19–274； UniProt 25–280 Author chain J； PDBConstruct 19–274； UniProt 25–280 Author chain K； PDBConstruct 19–274； UniProt 25–280 Author chain M； PDBConstruct 19–274； UniProt 25–280 Author chain N； PDBConstruct 19–274； UniProt 25–280 Author chain P； PDBConstruct 19–274； UniProt 25–280 Author chain Q； PDBConstruct 19–274； UniProt 25–280 Author chain S； PDBConstruct 19–274； UniProt 25–280 Author chain T； PDBConstruct 19–274； UniProt 25–280 Author chain V； PDBConstruct 19–274； UniProt 25–280 Author chain W； PDBConstruct 19–274； UniProt 25–280

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 9z7u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9z7u
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9z7u
Deposition date deposition_date2025-11-17
Structure title titleHuman Stomatin - C8 Symmetry
Keywords keywordsOligomer, C8 symmetry, scaffold, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier58.98 Å
Radius of gyration Rg (electron density) rg_electron58.88 Å
Forward intensity I(0) i02903830000.00
Molecular weight molecular_weight467700.0 kDa
Excluded volume excluded_volume592080 ų
Envelope volume envelope_volume1026300 ų
Hydration-shell volume shell_volume140420 ų
Envelope diameter envelope_diameter162.0 Å
Shell Rg shell_rg68.18 Å
Envelope Rg envelope_rg55.56 Å
Shape Rg shape_rg58.93 Å
Total Rg total_rg58.93 Å
Total atoms total_atoms32864
Residues n_residues4360
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 dmax153.4 Å
Rg (real space) rg_real58.53 Å
Rg uncertainty (real space) rg_real_error0.83 Å
I(0) (real space) i0_real2.9040e+09
I(0) uncertainty (real space) i0_real_error5.4950e+07
Rg (reciprocal space) rg_reciprocal59.33 Å
I(0) (reciprocal space) i0_reciprocal2907000000.0000
Solution quality estimate total_estimate0.8464
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary79.5 Å
Skewness Skewness skewness-0.127
Kurtosis Kurtosis kurtosis-0.811
Angular range angular_range— – 0.1350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha100400000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 1.000; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

9. Files and Curves (10)