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9zd2

C1 local refinement of aquaporin 1 bound to endogenous human stomatin

Method: ELECTRON MICROSCOPY Dmax: 130.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Aquaporin-1

OrganismNot specified

UniProt P29972

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain A； UniProt 3–249 Chain B； UniProt 3–249 Chain C； UniProt 3–249 Chain D； UniProt 3–249 Not recorded Stomatin × 5 （P27105） 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

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 9ZD2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1FQY STRUCTURE OF AQUAPORIN-1 AT 3.8 A RESOLUTION BY ELECTRON CRYSTALLOGRAPHY Deposited 2000-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–269（269 aa）
Not recorded No recorded non-water small molecule ELECTRON CRYSTALLOGRAPHY
X-ray crystallization conditions Dialysis with continuous flow dialysis machine；pH 6；298 K；Escherichia coli lipids, magnesium chloride, sodium chloride, MES, pH 6.0, Dialysis with continuous flow dialysis machine, temperature 298K
Resolution 3.80 Å R-free 0.417
1H6I A REFINED STRUCTURE OF HUMAN AQUAPORIN 1 Deposited 2001-06-15 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 1–269（269 aa）
Not recorded No recorded non-water small molecule ELECTRON CRYSTALLOGRAPHY mmCIF provides none of the parsed conditions Resolution 3.54 Å R-free 0.376
1IH5 CRYSTAL STRUCTURE OF AQUAPORIN-1 Deposited 2001-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–269（269 aa）
Not recorded No recorded non-water small molecule ELECTRON CRYSTALLOGRAPHY mmCIF provides none of the parsed conditions Resolution 3.70 Å R-free 0.458
4CSK human Aquaporin Deposited 2014-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–269（269 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；pH 9
Resolution 3.28 Å R-free 0.298
6POJ STRUCTURAL REFINEMENT OF AQUAPORIN 1 VIA SSNMR Deposited 2019-07-04 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 1–269（269 aa）
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 7；278 K；Ionic strength (raw mmCIF value) 10 mM NaCl；Pressure 1
NMR sample composition 2 w/v [U-13C; U-15N] AQUAPORIN 1, NMR buffer | NMR buffer
Resolution not provided
7UZE Erythrocyte ankyrin-1 complex class 2 local refinement of AQP1 (C4 symmetry applied) Deposited 2022-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–269（269 aa）
Chain B 1–269（269 aa）
Chain C 1–269（269 aa）
Chain D 1–269（269 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CLR CHOLESTEROL × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Final gel filtration buffer contained 0.05 % (w/v) digitonin, 130mM KCl, 20mM HEPES pH 7.4, 1mM ATP, 1mM MgCl2, 1mM PMSF. Peak fractions were concentrated to 8mg/mL, and 0.01% (w/v) of glycyrrhizic acid was added immediately prior to vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds.
Resolution 2.40 Å
8CT2 Local refinement of AQP1 tetramer (C1; refinement mask included D1 of protein 4.2 and Ankyrin-1 AR1-5) in Class 2 of erythrocyte ankyrin-1 complex Deposited 2022-05-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–269（269 aa）
Chain B 1–269（269 aa）
Chain C 1–269（269 aa）
Chain D 1–269（269 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CLR CHOLESTEROL × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds
Resolution 3.10 Å
8CTE Class 2 of erythrocyte ankyrin-1 complex (Composite map) Deposited 2022-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain M 1–269（269 aa）
Chain O 1–269（269 aa）
Chain R 1–269（269 aa）
Chain S 1–269（269 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CLR CHOLESTEROL × 10 AJP Digitonin × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds
Resolution 2.90 Å
9ZCZ C4 local refinement of stomatin-bound aquaporin (human) Deposited 2025-11-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 3–249（247 aa）
Chain B 3–249（247 aa）
Chain C 3–249（247 aa）
Chain D 3–249（247 aa）
Not recorded CLR CHOLESTEROL × 4 PLM PALMITIC ACID × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AQP1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–247； UniProt 3–249 Author chain B； PDBConstruct 1–247； UniProt 3–249 Author chain C； PDBConstruct 1–247； UniProt 3–249 Author chain D； PDBConstruct 1–247； UniProt 3–249

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain E； UniProt 25–200 Chain F； UniProt 25–200 Chain G； UniProt 25–200 Chain H； UniProt 25–200 Chain I； UniProt 25–200 Not recorded Aquaporin-1 × 4 （P29972） 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

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 9ZD2 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 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
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
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 2
Chains and sequence ranges Author chain E； PDBConstruct 19–194； UniProt 25–200 Author chain F； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 9zd2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9zd2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9zd2
Deposition date deposition_date2025-11-24
Structure title titleC1 local refinement of aquaporin 1 bound to endogenous human stomatin
Keywords keywordsOligomer, C8 symmetry, scaffold, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier42.68 Å
Radius of gyration Rg (electron density) rg_electron41.85 Å
Forward intensity I(0) i0567881000.00
Molecular weight molecular_weight209080.0 kDa
Excluded volume excluded_volume267560 ų
Envelope volume envelope_volume379880 ų
Hydration-shell volume shell_volume73723 ų
Envelope diameter envelope_diameter128.6 Å
Shell Rg shell_rg49.69 Å
Envelope Rg envelope_rg40.16 Å
Shape Rg shape_rg41.86 Å
Total Rg total_rg42.22 Å
Total atoms total_atoms14755
Residues n_residues1958
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax130.3 Å
Rg (real space) rg_real42.46 Å
Rg uncertainty (real space) rg_real_error0.87 Å
I(0) (real space) i0_real5.6790e+08
I(0) uncertainty (real space) i0_real_error9.5610e+06
Rg (reciprocal space) rg_reciprocal42.68 Å
I(0) (reciprocal space) i0_reciprocal568000000.0000
Solution quality estimate total_estimate0.8343
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary52.8 Å
Skewness Skewness skewness0.006
Kurtosis Kurtosis kurtosis-0.769
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha60200000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)