7kh0

Cryo-EM structure of the human arginine vasopressin AVP-vasopressin receptor V2R-Gs signaling complex

Method: ELECTRON MICROSCOPY Dmax: 126.4 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 Insufficient information Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain R; UniProt 1–371 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) ;Guanine nucleotide-binding protein G(i) subunit alpha-3, Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short fusion ; × 1 (P08754,P63092-2) Arg-vasopressin × 1 (P01185) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Single Fab chain (scFv16) × 1 Nanobody 35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

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 10–380; UniProt 1–371

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

Homo sapiens

UniProt P62873

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 × 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(i) subunit alpha-3, Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short fusion ; × 1 (P08754,P63092-2) Arg-vasopressin × 1 (P01185) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Single Fab chain (scFv16) × 1 Nanobody 35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

1260 other PDB entries and 1263 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 12–350; UniProt 2–340

;Guanine nucleotide-binding protein G(i) subunit alpha-3, Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short fusion ;

Homo sapiens

UniProt P08754

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 2–18 Not recorded Vasopressin V2 receptor × 1 (P30518) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Arg-vasopressin × 1 (P01185) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Single Fab chain (scFv16) × 1 Nanobody 35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

24 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI3_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 1–17; UniProt 2–18

;Guanine nucleotide-binding protein G(i) subunit alpha-3, Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short fusion ;

Homo sapiens

UniProt P63092-2

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 26–380 Not recorded Vasopressin V2 receptor × 1 (P30518) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Arg-vasopressin × 1 (P01185) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Single Fab chain (scFv16) × 1 Nanobody 35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAS2-2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 18–372; UniProt 26–380

Arg-vasopressin

Homo sapiens

UniProt P01185

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain L; UniProt 20–28 Non-standard monomer:Yes (specific site not provided by mmCIF) Vasopressin V2 receptor × 1 (P30518) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) ;Guanine nucleotide-binding protein G(i) subunit alpha-3, Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short fusion ; × 1 (P08754,P63092-2) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Single Fab chain (scFv16) × 1 Nanobody 35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name NEU2_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain L; PDBConstruct 1–9; UniProt 20–28

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

Homo sapiens

UniProt P59768

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain G; UniProt 2–68 Not recorded Vasopressin V2 receptor × 1 (P30518) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) ;Guanine nucleotide-binding protein G(i) subunit alpha-3, Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short fusion ; × 1 (P08754,P63092-2) Arg-vasopressin × 1 (P01185) Single Fab chain (scFv16) × 1 Nanobody 35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

1233 other PDB entries and 1236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain G; PDBConstruct 1–67; UniProt 2–68

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 7kh0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7kh0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7kh0
Deposition date deposition_date2020-10-19
Structure title titleCryo-EM structure of the human arginine vasopressin AVP-vasopressin receptor V2R-Gs signaling complex
Keywords keywordsarginine vasopressin AVP, Gs, signaling complex, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier38.60
Radius of gyration Rg (electron density) rg_electron38.58
Forward intensity I(0) i0303889000.00
Molecular weight molecular_weight140880.0 kDa
Excluded volume excluded_volume176060 ų
Envelope volume envelope_volume236280 ų
Hydration-shell volume shell_volume52247 ų
Envelope diameter envelope_diameter130.5
Shell Rg shell_rg43.11
Envelope Rg envelope_rg38.37
Shape Rg shape_rg38.58
Total Rg total_rg38.86
Total atoms total_atoms9898
Residues n_residues1273
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 dmax126.4
Rg (real space) rg_real38.57
Rg uncertainty (real space) rg_real_error1.17
I(0) (real space) i0_real3.0390e+08
I(0) uncertainty (real space) i0_real_error5.3830e+06
Rg (reciprocal space) rg_reciprocal38.60
I(0) (reciprocal space) i0_reciprocal303900000.0000
Solution quality estimate total_estimate0.8973
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.2
Skewness Skewness skewness0.257
Kurtosis Kurtosis kurtosis-0.540
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha55040000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.890

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd7kh0b_
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.4 — WD40 repeat-like
Family Family familyb.69.4.1 — WD40-repeat
Domain ID domain_idd7kh0g_
Class classa — All alpha proteins
Fold Fold folda.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamilya.137.3 — Transducin (heterotrimeric G protein), gamma chain
Family Family familya.137.3.1 — Transducin (heterotrimeric G protein), gamma chain
Domain ID domain_idd7kh0n1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd7kh0n2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd7kh0s1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd7kh0s2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id7kh0B01
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_id7kh0N01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)