7wbj

Cryo-EM structure of N-terminal modified human vasoactive intestinal polypeptide receptor 2 (VIP2R) in complex with PACAP27 and Gs

Method: ELECTRON MICROSCOPY Dmax: 149.7 Å Quality: GOOD

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

Vasoactive intestinal polypeptide receptor 2

Homo sapiens

UniProt P41587

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain R; UniProt 24–438 Not recorded Pituitary adenylate cyclase-activating polypeptide 27 × 1 (P18509) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P04896) 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) Nanobody-35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.42 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.

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VIPR2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 18–432; UniProt 24–438

Pituitary adenylate cyclase-activating polypeptide 27

OrganismNot specified

UniProt P18509

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain L; UniProt 132–158 Not recorded Vasoactive intestinal polypeptide receptor 2 × 1 (P41587) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P04896) 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) Nanobody-35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.42 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.

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PACA_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain L; PDBConstruct 1–27; UniProt 132–158

Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

Bos taurus

UniProt P04896

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–394 Mutation:S54N, G226A, E268A, N271K, K274D, R280K, T284D, I285T, A366S Vasoactive intestinal polypeptide receptor 2 × 1 (P41587) Pituitary adenylate cyclase-activating polypeptide 27 × 1 (P18509) 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) Nanobody-35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.42 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.

41 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAS2_BOVIN
Isoform
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 1–394; UniProt 1–394

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Vasoactive intestinal polypeptide receptor 2 × 1 (P41587) Pituitary adenylate cyclase-activating polypeptide 27 × 1 (P18509) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P04896) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Nanobody-35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.42 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 4
Chains and sequence ranges Author chain B; PDBConstruct 36–374; 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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Vasoactive intestinal polypeptide receptor 2 × 1 (P41587) Pituitary adenylate cyclase-activating polypeptide 27 × 1 (P18509) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P04896) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Nanobody-35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.42 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 5
Chains and sequence ranges Author chain G; 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 7wbj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7wbj
Deposition date deposition_date2021-12-16
Structure title titleCryo-EM structure of N-terminal modified human vasoactive intestinal polypeptide receptor 2 (VIP2R) in complex with PACAP27 and Gs
Keywords keywordsvasoactive intestinal polypeptide receptor 2, G protein-coupled receptor, ligand recognition, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier41.03
Radius of gyration Rg (electron density) rg_electron41.16
Forward intensity I(0) i0248736000.00
Molecular weight molecular_weight127830.0 kDa
Excluded volume excluded_volume159870 ų
Envelope volume envelope_volume218810 ų
Hydration-shell volume shell_volume47661 ų
Envelope diameter envelope_diameter157.9
Shell Rg shell_rg42.75
Envelope Rg envelope_rg42.04
Shape Rg shape_rg41.15
Total Rg total_rg41.28
Total atoms total_atoms8989
Residues n_residues1146
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 dmax149.7
Rg (real space) rg_real41.62
Rg uncertainty (real space) rg_real_error1.69
I(0) (real space) i0_real2.4870e+08
I(0) uncertainty (real space) i0_real_error4.1640e+06
Rg (reciprocal space) rg_reciprocal41.04
I(0) (reciprocal space) i0_reciprocal248600000.0000
Solution quality estimate total_estimate0.7592
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.5
Skewness Skewness skewness0.774
Kurtosis Kurtosis kurtosis0.138
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44540000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.503; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.739; Smooth: 0.619

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id7wbjB01
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_id7wbjN01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7wbjR01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins

8. Citations (1)

9. Files and Curves (10)