7vuj

Cryo-EM structure of a class A orphan GPCR

Method: ELECTRON MICROSCOPY Dmax: 114.4 Å Quality: GOOD

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

Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 5–64 Chain A; UniProt 190–357 Mutation:G49D, E50N, A235D, S238D Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nanobody 35 × 1 chimera of Endo-1,4-beta-xylanase and Probable G-protein coupled receptor 139 × 1 (P09850,Q6DWJ6) MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.80 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 1
Chains and sequence ranges Author chain A; PDBConstruct 13–72; UniProt 5–64 Author chain A; PDBConstruct 81–238; UniProt 190–357

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092-2) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nanobody 35 × 1 chimera of Endo-1,4-beta-xylanase and Probable G-protein coupled receptor 139 × 1 (P09850,Q6DWJ6) MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.80 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 8–346; UniProt 2–340

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092-2) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Nanobody 35 × 1 chimera of Endo-1,4-beta-xylanase and Probable G-protein coupled receptor 139 × 1 (P09850,Q6DWJ6) MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.80 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 3
Chains and sequence ranges Author chain G; PDBConstruct 1–71; UniProt 1–71

chimera of Endo-1,4-beta-xylanase and Probable G-protein coupled receptor 139

Homo sapiens

UniProt P09850

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 29–213 Mutation:D39F, R150D, S62V Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092-2) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nanobody 35 × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.80 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.

32 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XYNA_BACCI
Isoform
PDB entities 5
Chains and sequence ranges Author chain R; PDBConstruct 29–213; UniProt 29–213

chimera of Endo-1,4-beta-xylanase and Probable G-protein coupled receptor 139

Homo sapiens

UniProt Q6DWJ6

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 2–321 Mutation:D39F, R150D, S62V Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092-2) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nanobody 35 × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.80 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.

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

View Construct and Data Evidence
UniProt name GP139_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain R; PDBConstruct 214–533; UniProt 2–321

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 7vuj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7vuj
Deposition date deposition_date2021-11-02
Structure title titleCryo-EM structure of a class A orphan GPCR
Keywords keywordsOrphan G protein coupled-receptor, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier34.14
Radius of gyration Rg (electron density) rg_electron34.16
Forward intensity I(0) i0212520000.00
Molecular weight molecular_weight117810.0 kDa
Excluded volume excluded_volume147790 ų
Envelope volume envelope_volume191370 ų
Hydration-shell volume shell_volume47130 ų
Envelope diameter envelope_diameter123.9
Shell Rg shell_rg40.21
Envelope Rg envelope_rg34.31
Shape Rg shape_rg34.17
Total Rg total_rg34.57
Total atoms total_atoms8286
Residues n_residues1034
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 dmax114.4
Rg (real space) rg_real34.20
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real2.1250e+08
I(0) uncertainty (real space) i0_real_error3.5640e+06
Rg (reciprocal space) rg_reciprocal34.16
I(0) (reciprocal space) i0_reciprocal212500000.0000
Solution quality estimate total_estimate0.8719
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.3
Skewness Skewness skewness0.437
Kurtosis Kurtosis kurtosis-0.187
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha61270000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.806

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_id7vujA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id7vujB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

8. Citations (1)

9. Files and Curves (10)