7dw9

Cryo-EM structure of human V2 vasopressin receptor in complex with an Gs protein

Method: ELECTRON MICROSCOPY Dmax: 126.0 Å Quality: GOOD

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

Vasopressin V2 receptor

Homo sapiens

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 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain R; UniProt 1–371 Not recorded Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Nanobody35 × 1 scFv16 × 1 CYS-TYR-PHE-GLN-ASN-CYS-PRO-ARG-GLY-NH2 × 1 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.60 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 1
Chains and sequence ranges Author chain R; PDBConstruct 117–487; UniProt 1–371

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Rattus norvegicus

UniProt P54311

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Vasopressin V2 receptor × 1 (P30518) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Nanobody35 × 1 scFv16 × 1 CYS-TYR-PHE-GLN-ASN-CYS-PRO-ARG-GLY-NH2 × 1 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.60 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.

161 other PDB entries and 162 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_RAT
Isoform
PDB entities 3
Chains and sequence ranges Author chain B; PDBConstruct 7–345; UniProt 2–340

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Bos taurus

UniProt P63212

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain Y; UniProt 1–71 Not recorded Vasopressin V2 receptor × 1 (P30518) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Nanobody35 × 1 scFv16 × 1 CYS-TYR-PHE-GLN-ASN-CYS-PRO-ARG-GLY-NH2 × 1 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.60 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.

215 other PDB entries and 216 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_BOVIN
Isoform
PDB entities 4
Chains and sequence ranges Author chain Y; PDBConstruct 1–71; UniProt 1–71

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 7dw9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7dw9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7dw9
Deposition date deposition_date2021-01-15
Structure title titleCryo-EM structure of human V2 vasopressin receptor in complex with an Gs protein
Keywords keywordsV2R, GPCR, Cryo-EM, AVP, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier38.75
Radius of gyration Rg (electron density) rg_electron38.78
Forward intensity I(0) i0311537000.00
Molecular weight molecular_weight143740.0 kDa
Excluded volume excluded_volume180070 ų
Envelope volume envelope_volume238650 ų
Hydration-shell volume shell_volume52509 ų
Envelope diameter envelope_diameter128.9
Shell Rg shell_rg43.22
Envelope Rg envelope_rg38.49
Shape Rg shape_rg38.77
Total Rg total_rg39.10
Total atoms total_atoms10105
Residues n_residues1283
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 dmax126.0
Rg (real space) rg_real38.73
Rg uncertainty (real space) rg_real_error1.00
I(0) (real space) i0_real3.1150e+08
I(0) uncertainty (real space) i0_real_error5.8300e+06
Rg (reciprocal space) rg_reciprocal38.75
I(0) (reciprocal space) i0_reciprocal311500000.0000
Solution quality estimate total_estimate0.8954
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.1
Skewness Skewness skewness0.261
Kurtosis Kurtosis kurtosis-0.543
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha49740000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.839

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7dw9B01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id7dw9N01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)