6hh0

Yeast V-ATPase transmembrane helix 7 NMR structure in DPC micelles

Method: SOLUTION NMR Dmax: 43.2 Å Quality: REASONABLE

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

V-type proton ATPase subunit a, vacuolar isoform

Saccharomyces cerevisiae

UniProt P32563

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 728–748 Fragment:transmembrane helix 7 No other associated polymer SOLUTION NMR NMR measurement conditions:pH 5;298 K;Ionic strength (raw mmCIF value) 50;Pressure ambient NMR sample composition:100 mM [U-99% 2H] Deuterated DPC, 50 mM potassium phosphate, 0.02 % sodium azide, 1 mM 13C and 15N labeled aminoacids 8 and 12 TM7 peptide, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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.

31 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VPH1_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–23; UniProt 728–748

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 6hh0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6hh0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6hh0
Deposition date deposition_date2018-08-24
Structure title titleYeast V-ATPase transmembrane helix 7 NMR structure in DPC micelles
Keywords keywordsATPasse, transmembrane helix, DPC micelle, NMR spectroscopy, membrane protein; MEMBRANE PROTEIN
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier10.57
Radius of gyration Rg (electron density) rg_electron10.94
Forward intensity I(0) i011077700.00
Molecular weight molecular_weight28304.0 kDa
Excluded volume excluded_volume36173 ų
Envelope volume envelope_volume8303 ų
Hydration-shell volume shell_volume6326 ų
Envelope diameter envelope_diameter45.2
Shell Rg shell_rg16.90
Envelope Rg envelope_rg13.51
Shape Rg shape_rg10.81
Total Rg total_rg11.85
Total atoms total_atoms4170
Residues n_residues250
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 dmax43.2
Rg (real space) rg_real10.82
Rg uncertainty (real space) rg_real_error0.67
I(0) (real space) i0_real1.1080e+07
I(0) uncertainty (real space) i0_real_error1.3630e+05
Rg (reciprocal space) rg_reciprocal10.81
I(0) (reciprocal space) i0_reciprocal11080000.0000
Solution quality estimate total_estimate0.6450
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary6.6
Skewness Skewness skewness0.534
Kurtosis Kurtosis kurtosis-0.518
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3225.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.145; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.006; Smooth: 0.940

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

8. Citations (1)

9. Files and Curves (10)