SAXSdb — 9pfz

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

Non-selective voltage-gated ion channel VDAC1

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–283	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7；25 mM NaPi, 100 mM NaCl, pH 7.0 cryo-EM vitrification conditions：Cryogen ETHANE；3.0 uL sample, blot time 3sec, Blotforce 1, Blot total 1,	Resolution 5.40 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.

Other PDB	Difference from Current Entry 9PFZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JK4 Structure of the human voltage-dependent anion channel Deposited 2008-08-15	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–283（282 aa） Fragment：RESIDUES 2-283	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1 M HEPES SODIUM PH 7.5, 30% V/V POLYETHYLENE GLYCOL 400	Resolution 4.10 Å R-free 0.387
2K4T Solution structure of human VDAC-1 in LDAO micelles Deposited 2008-06-17	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–283（283 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 25；Pressure AMBIENT NMR sample composition 1 mM [U-13C; U-15N; U-2H] VDAC-1, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
5JDP E73V mutant of the human voltage-dependent anion channel Deposited 2016-04-17	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–283（282 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；310 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition 0.8 mM U- 2H, 15N_sample E73V mutant of the Voltage-dependent anion channel 1, 2 % [U-2H] LDAO, 20 mM [U-2H] TRIS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5XDN Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in P22121 space group Deposited 2017-03-28	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 × 2 PDB declaration: dimeric	Chain A 1–283（283 aa） Chain B 1–283（283 aa）	Not recorded	D12 DODECANE × 2 HEX HEXANE × 4 OCT N-OCTANE × 1 D10 DECANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；36% PEG300, 0.1 M MES (pH 6.5), 0.1 M NaCl	Resolution 3.15 Å R-free 0.300
5XDO Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group Deposited 2017-03-28	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 × 2 PDB declaration: dimeric	Chain A 1–283（283 aa） Chain B 1–283（283 aa）	Not recorded	SPD SPERMIDINE × 2 OCT N-OCTANE × 4 LNK PENTANE × 2 HEX HEXANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；45% PEG300, 0.1 M HEPES (pH 7.0), 0.15 M NaCl, 11 mM spermidine	Resolution 3.10 Å R-free 0.298
6G6U The dynamic nature of the VDAC1 channels in bilayers: human VDAC1 at 2.7 Angstrom resolution Deposited 2018-04-03	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 × 2 PDB declaration: dimeric	Chain A 1–283（283 aa） Chain B 1–283（283 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 3 NO3 NITRATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；25.5% precipitant mix 4 [25% (v/v) MPD, 25% (w/v) PEG 1000, 25% (w/v) PEG 3350], 0.06 M NH4NO3, 0.1 buffer system 1 [imidazole and MES adjusted to pH 6.5]	Resolution 2.74 Å R-free 0.287
6G73 The dynamic nature of the VDAC1 channels in bilayers: human VDAC1 at 3.3 Angstrom resolution Deposited 2018-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–283（283 aa） Chain D 1–283（283 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292.2 K；25.5% Precipitant mix 4 [precipitant mix 4 consists of 25% (v/v) MPD, 25% (w/v) PEG1000, 25% (w/v) PEG3350], 0.06M NaNO3, 0.08M K2HPO4, 0.1M Buffer System2 [HEPES and MOPS adjusted to pH 7.5]	Resolution 3.27 Å R-free 0.298
6G73 The dynamic nature of the VDAC1 channels in bilayers: human VDAC1 at 3.3 Angstrom resolution Deposited 2018-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–283（283 aa） Chain B 1–283（283 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292.2 K；25.5% Precipitant mix 4 [precipitant mix 4 consists of 25% (v/v) MPD, 25% (w/v) PEG1000, 25% (w/v) PEG3350], 0.06M NaNO3, 0.08M K2HPO4, 0.1M Buffer System2 [HEPES and MOPS adjusted to pH 7.5]	Resolution 3.27 Å R-free 0.298
6TIQ Refined solution NMR structure of hVDAC-1 in detergent micelles Deposited 2019-11-22	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–283（283 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303.15 K；Ionic strength (raw mmCIF value) 225；Pressure 1 NMR sample composition 0.6 mM U-99%-2H,13C,15N hVDAC-1, 3 % no LDAO, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.6 mM [ U -99%- 2 H, 13 C, 15 N; 99%- 1 H delta -IL; 99%- 1 H gamma -V] hVDAC-1, 3 % [U-99% 2H] LDAO, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.6 mM [ U -99%- 2 H, 15 N; 99%- 1 H delta , 13 C delta -IL; 99%- 1 H gamma , 13 C gamma -V] hVDAC-1, 3 % [U-99% 2H] LDAO, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6TIR NOE based model of hVDAC-1 bound to beta-NADH in detergent micelles Deposited 2019-11-22	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 1–283（283 aa）	Not recorded	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1	SOLUTION NMR NMR measurement conditions pH 6.5；303.15 K；Ionic strength (raw mmCIF value) 25；Pressure 1 NMR sample composition 0.5 mM [U-99%-2H, 15N; 99%-1Hdelta-IL; 99%-1Hgamma-V] human VDAC-1, 45 mM beta-NADH, 150 mM [U-99% 2H] LDAO, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-99%-2H, 15N; 99%-1H,13C-delta-IL; 99%-1H,13Cgamma-V] human VDAC-1, 45 mM beta-NADH, 150 mM [U-99% 2H] LDAO, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM U-99%-2H,15N,13C human VDAC-1, 150 mM [U-99% 2H] LDAO, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7QI2 Magic-angle spinning NMR structure of the human voltage-dependent anion channel 1 (E73V/C127A/C232S) in DMPC lipid bilayers Deposited 2021-12-14	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–283（283 aa）	Mutation：E73V/C127A/C232S	No recorded non-water small molecule	SOLID-STATE NMR NMR measurement conditions pH 6.5；285 K；Ionic strength (raw mmCIF value) 0.21；Pressure 1 NMR sample composition 66 % w/w [U-13C; U-15N; U-2H] u[2H,13C,15N]-hVDAC1(E73V/C127A/C232S), 33 % w/w DMPC, 10 mM MES, 150 mM sodium chloride, 20 mM MgCl2, 100% H2O \| 100% H2O NMR sample composition 66 % w/w [U-13C; U-15N]-alpha PET u[2H,13C,15N]-hVDAC1(E73V/C127A/C232S), 33 % w/w DMPC, 10 mM MES, 150 mM sodium chloride, 20 mM MgCl2, 100% H2O \| 100% H2O	Resolution not provided
8J0O cryo-EM structure of human EMC and VDAC Deposited 2023-04-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain K 1–283（283 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.32 Å

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VDAC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–283； UniProt 1–283

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	9pfz
Deposition date deposition_date	2025-07-07
Structure title title	Architecture of human Voltage Dependent Anion Channel 1 in nanodiscs
Keywords keywords	Beta-barrel, mitochondrial outer membrane protein, lipid bilayer nanodisc, MEMBRANE PROTEIN; 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	22.21 Å
Radius of gyration Rg (electron density) rg_electron	21.48 Å
Forward intensity I(0) i0	16674900.00
Molecular weight molecular_weight	30776.0 kDa
Excluded volume excluded_volume	38549 Å³
Envelope volume envelope_volume	54986 Å³
Hydration-shell volume shell_volume	21604 Å³
Envelope diameter envelope_diameter	71.2 Å
Shell Rg shell_rg	28.12 Å
Envelope Rg envelope_rg	20.60 Å
Shape Rg shape_rg	21.48 Å
Total Rg total_rg	22.42 Å
Total atoms total_atoms	4316
Residues n_residues	283
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	66.6 Å
Rg (real space) rg_real	22.02 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	1.6670e+07
I(0) uncertainty (real space) i0_real_error	1.9010e+05
Rg (reciprocal space) rg_reciprocal	22.07 Å
I(0) (reciprocal space) i0_reciprocal	16680000.0000
Solution quality estimate total_estimate	0.7834
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.8 Å
Skewness Skewness skewness	-0.114
Kurtosis Kurtosis kurtosis	-0.437
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1879000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.733; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; 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	5.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	202865

Description description	Non-selective voltage-gated ion channel VDAC1
Molecular weight formula_weight	30807.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4316

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/pf/9pfz/9pfz.fit
pddf	/app/data/pr_computation/pf/9pfz/9pfz.pr.out
profile	/app/data/saxs_computation/pf/9pfz/9pfz.dat

Architecture of human Voltage Dependent Anion Channel 1 in nanodiscs

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

Non-selective voltage-gated ion channel VDAC1

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)