2nvj

NMR structures of transmembrane segment from subunit a from the yeast proton V-ATPase

Method: SOLUTION NMR Dmax: 44.8 Å Quality: REASONABLE

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

25mer peptide from Vacuolar ATP synthase subunit a, vacuolar isoform

OrganismNot specified

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 720–744 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions:303 K;Pressure ambient NMR sample composition:2mM sMTM7 peptide (natural abundance labeling); 100% d6-DMSO | 100% d6-DMSO 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 1–25; UniProt 720–744

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 2nvj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2nvj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2nvj
Deposition date deposition_date2006-11-13
Structure title titleNMR structures of transmembrane segment from subunit a from the yeast proton V-ATPase
Keywords keywordsalfa helix, 3, 10 helix, pi helix, HYDROLASE; HYDROLASE
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier10.83
Radius of gyration Rg (electron density) rg_electron10.78
Forward intensity I(0) i048656600.00
Molecular weight molecular_weight56685.0 kDa
Excluded volume excluded_volume70666 ų
Envelope volume envelope_volume19673 ų
Hydration-shell volume shell_volume11746 ų
Envelope diameter envelope_diameter49.4
Shell Rg shell_rg20.19
Envelope Rg envelope_rg15.15
Shape Rg shape_rg10.76
Total Rg total_rg11.46
Total atoms total_atoms7840
Residues n_residues500
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 dmax44.8
Rg (real space) rg_real11.01
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real4.8660e+07
I(0) uncertainty (real space) i0_real_error5.5570e+05
Rg (reciprocal space) rg_reciprocal11.00
I(0) (reciprocal space) i0_reciprocal48660000.0000
Solution quality estimate total_estimate0.7240
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary9.6
Skewness Skewness skewness0.589
Kurtosis Kurtosis kurtosis-0.109
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12940.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.453; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.072; Smooth: 0.977

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

8. Citations (1)

9. Files and Curves (10)