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9xb1

Cryo-EM structure of human V1aR in apo state at a resolution of 2.8 angstrom

Method: ELECTRON MICROSCOPY Dmax: 89.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Vasopressin V1a receptor

Homo sapiens

UniProt P37288

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 33–418 Chain B； UniProt 33–418 Mutation：S341C, N344K CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.80 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 9XB1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1YTV Maltose-binding protein fusion to a C-terminal fragment of the V1a vasopressin receptor Deposited 2005-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain M 362–420（59 aa） Fragment：linker + residues 362-418
Chain N 362–420（59 aa） Fragment：linker + residues 362-418
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.2M Ammonium sulfate, 25%(v/v)PEG 400 and 25%(v/v) glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.80 Å R-free 0.225
9UWI Cryo-EM structure of human V1aR bound with atosiban at a resolution of 2.8 angstrom Deposited 2025-05-12 Different mutation/modification Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 33–418（386 aa）
Chain B 33–418（386 aa）
Not recorded CLR CHOLESTEROL × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9UWJ Cryo-EM structure of human V1aR bound with balovaptan at a resolution of 3.0 angstrom Deposited 2025-05-12 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 33–418（386 aa）
Chain B 33–418（386 aa）
Not recorded A1EB7 Balovaptan × 2 CLR CHOLESTEROL × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9UWL Cryo-EM structure of human V1aR bound with SRX246 at a resolution of 2.6 angstrom Deposited 2025-05-12 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 33–418（386 aa）
Chain B 33–418（386 aa）
Not recorded A1EQN SRX246 × 2 CLR CHOLESTEROL × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name V1AR_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–386； UniProt 33–418 Author chain B； PDBConstruct 1–386； UniProt 33–418

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 9xb1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9xb1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9xb1
Deposition date deposition_date2025-10-23
Structure title titleCryo-EM structure of human V1aR in apo state at a resolution of 2.8 angstrom
Keywords keywordsGPCR, small molecule, antagonist, nanobody, SIGNALING PROTEIN, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.90 Å
Radius of gyration Rg (electron density) rg_electron27.19 Å
Forward intensity I(0) i047979100.00
Molecular weight molecular_weight59486.0 kDa
Excluded volume excluded_volume76738 ų
Envelope volume envelope_volume91873 ų
Hydration-shell volume shell_volume28095 ų
Envelope diameter envelope_diameter94.3 Å
Shell Rg shell_rg34.18 Å
Envelope Rg envelope_rg27.37 Å
Shape Rg shape_rg27.19 Å
Total Rg total_rg27.96 Å
Total atoms total_atoms8416
Residues n_residues512
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax89.2 Å
Rg (real space) rg_real27.86 Å
Rg uncertainty (real space) rg_real_error0.58 Å
I(0) (real space) i0_real4.7980e+07
I(0) uncertainty (real space) i0_real_error6.2600e+05
Rg (reciprocal space) rg_reciprocal27.88 Å
I(0) (reciprocal space) i0_reciprocal47980000.0000
Solution quality estimate total_estimate0.7163
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary87.6 Å
Skewness Skewness skewness0.208
Kurtosis Kurtosis kurtosis-0.632
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8087000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 0.177; Positv: 1.000; Valcen: 0.978; Smooth: 0.963
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)