4ix9

Crystal structure of subunit F of V-ATPase from S. cerevisiae

Method: X-RAY DIFFRACTION Dmax: 77.2 Å Quality: EXCELLENT

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

V-type proton ATPase subunit F

Saccharomyces cerevisiae

UniProt P39111

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 1–94 Fragment:Coupling and Regulatory Subunit F, UNP residues 1-94 Mutation:I69M Non-standard monomer:Yes (specific site not provided by mmCIF) TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.8;291 K;30% PEG 4000, 0.05M MgCl2,6H2O, 0.1M Tris HCl pH 8.8, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.33 Å R-free 0.212
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–94 Fragment:Coupling and Regulatory Subunit F, UNP residues 1-94 Mutation:I69M Non-standard monomer:Yes (specific site not provided by mmCIF) TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.8;291 K;30% PEG 4000, 0.05M MgCl2,6H2O, 0.1M Tris HCl pH 8.8, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.33 Å R-free 0.212
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–94 Fragment:Coupling and Regulatory Subunit F, UNP residues 1-94 Mutation:I69M Non-standard monomer:Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.8;291 K;30% PEG 4000, 0.05M MgCl2,6H2O, 0.1M Tris HCl pH 8.8, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.33 Å R-free 0.212
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1–94 Fragment:Coupling and Regulatory Subunit F, UNP residues 1-94 Mutation:I69M Non-standard monomer:Yes (specific site not provided by mmCIF) TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.8;291 K;30% PEG 4000, 0.05M MgCl2,6H2O, 0.1M Tris HCl pH 8.8, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.33 Å R-free 0.212

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.

19 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATF_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–94; UniProt 1–94 Author chain B; PDBConstruct 1–94; UniProt 1–94 Author chain C; PDBConstruct 1–94; UniProt 1–94 Author chain D; PDBConstruct 1–94; UniProt 1–94

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 4ix9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ix9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ix9
Deposition date deposition_date2013-01-24
Structure title titleCrystal structure of subunit F of V-ATPase from S. cerevisiae
Keywords keywordsV-ATPase, stalk subunit, subunit F, Rossmann fold, Regulatory, coupling, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.30
Radius of gyration Rg (electron density) rg_electron24.56
Forward intensity I(0) i031166800.00
Molecular weight molecular_weight42720.0 kDa
Excluded volume excluded_volume53425 ų
Envelope volume envelope_volume67765 ų
Hydration-shell volume shell_volume23750 ų
Envelope diameter envelope_diameter78.7
Shell Rg shell_rg30.81
Envelope Rg envelope_rg24.09
Shape Rg shape_rg24.55
Total Rg total_rg25.38
Total atoms total_atoms2996
Residues n_residues363
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax77.2
Rg (real space) rg_real25.22
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real3.1170e+07
I(0) uncertainty (real space) i0_real_error4.0940e+05
Rg (reciprocal space) rg_reciprocal25.24
I(0) (reciprocal space) i0_reciprocal31170000.0000
Solution quality estimate total_estimate0.9163
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.6
Skewness Skewness skewness0.145
Kurtosis Kurtosis kurtosis-0.614
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3311000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.980

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4ix9A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10580 — ATPase, V1 complex, subunit F
Domain ID domain_id4ix9B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10580 — ATPase, V1 complex, subunit F
Domain ID domain_id4ix9C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10580 — ATPase, V1 complex, subunit F
Domain ID domain_id4ix9D00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10580 — ATPase, V1 complex, subunit F

8. Citations (1)

9. Files and Curves (10)