9hap

Cryo-EM structure of inactive human arginine-vasopressin (AVP) V2 receptor (V2R) with tolvaptan

Method: ELECTRON MICROSCOPY Dmax: 142.9 Å Quality: GOOD

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

Vasopressin V2 receptor,Soluble cytochrome b562

Escherichia coli

UniProt P0ABE7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain R; UniProt 23–123 Not recorded Synthetic antibody, anti-BRIL Fab fragment, Heavy chain × 1 anti-BRIL Fab Nanobody × 1 Synthetic antibody, anti-BRIL Fab fragment, Light chain × 1 A1IT8 (R)-Tolvaptan × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.50 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.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 4
Chains and sequence ranges Author chain R; PDBConstruct 441–541; UniProt 23–123

Vasopressin V2 receptor,Soluble cytochrome b562

Escherichia coli

UniProt P30518

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain R; UniProt 4–371 Not recorded Synthetic antibody, anti-BRIL Fab fragment, Heavy chain × 1 anti-BRIL Fab Nanobody × 1 Synthetic antibody, anti-BRIL Fab fragment, Light chain × 1 A1IT8 (R)-Tolvaptan × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.50 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.

36 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name V2R_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain R; PDBConstruct 68–435; UniProt 4–371

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 9hap

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9hap
Deposition date deposition_date2024-11-04
最后修订 last_revision2025-06-04
Structure title titleCryo-EM structure of inactive human arginine-vasopressin (AVP) V2 receptor (V2R) with tolvaptan
Keywords keywordsGPCR, V2R, TVP, tolvaptan, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier41.12
Radius of gyration Rg (electron density) rg_electron41.48
Forward intensity I(0) i0273085000.00
Molecular weight molecular_weight89313.0 kDa
Excluded volume excluded_volume86286 ų
Envelope volume envelope_volume174180 ų
Hydration-shell volume shell_volume37665 ų
Envelope diameter envelope_diameter145.6
Shell Rg shell_rg42.78
Envelope Rg envelope_rg41.07
Shape Rg shape_rg41.47
Total Rg total_rg41.55
Total atoms total_atoms6767
Residues n_residues901
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 dmax142.9
Rg (real space) rg_real41.44
Rg uncertainty (real space) rg_real_error1.68
I(0) (real space) i0_real2.7310e+08
I(0) uncertainty (real space) i0_real_error5.2970e+06
Rg (reciprocal space) rg_reciprocal41.13
I(0) (reciprocal space) i0_reciprocal273000000.0000
Solution quality estimate total_estimate0.8261
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.9
Skewness Skewness skewness0.449
Kurtosis Kurtosis kurtosis-0.503
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8808000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.733; Smooth: 0.670

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)