5vai

Cryo-EM structure of the activated Glucagon-like peptide-1 receptor in complex with G protein

Method: ELECTRON MICROSCOPY Dmax: 153.3 Å Quality: REASONABLE

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

Uncharacterized protein

Oryctolagus cuniculus

UniProt G1SGD4

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 24–422 Not recorded Glucagon-like peptide 1 × 1 (P01275) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) 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 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.10 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 G1SGD4_RABIT
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 63–461; UniProt 24–422

Glucagon-like peptide 1

OrganismNot specified

UniProt P01275

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 P; UniProt 98–128 Fragment:UNP residues 98-128 Uncharacterized protein × 1 (G1SGD4) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) 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 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.10 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.

33 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GLUC_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain P; PDBConstruct 1–31; UniProt 98–128

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

Homo sapiens

UniProt P63092

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 1–380 Fragment:UNP residuews 1-380 Uncharacterized protein × 1 (G1SGD4) Glucagon-like peptide 1 × 1 (P01275) 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 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.10 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.

348 other PDB entries and 356 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAS2_HUMAN
Isoform P63092-2
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 1–380; UniProt 1–380

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 Uncharacterized protein × 1 (G1SGD4) Glucagon-like peptide 1 × 1 (P01275) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) nanobody 35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.10 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 13–351; 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 1–68 Fragment:UNP residues 1-68 Uncharacterized protein × 1 (G1SGD4) Glucagon-like peptide 1 × 1 (P01275) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) nanobody 35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.10 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 1–68; UniProt 1–68

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 5vai

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5vai
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5vai
Deposition date deposition_date2017-03-27
Structure title titleCryo-EM structure of the activated Glucagon-like peptide-1 receptor in complex with G protein
Keywords keywordsClass B GPCR, GLP-1, GLP-1R, Complex, Signaling Protein-Hormone complex; Signaling Protein/Hormone
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier40.73
Radius of gyration Rg (electron density) rg_electron40.75
Forward intensity I(0) i0256702000.00
Molecular weight molecular_weight129250.0 kDa
Excluded volume excluded_volume161360 ų
Envelope volume envelope_volume216090 ų
Hydration-shell volume shell_volume47906 ų
Envelope diameter envelope_diameter163.6
Shell Rg shell_rg42.13
Envelope Rg envelope_rg41.87
Shape Rg shape_rg40.78
Total Rg total_rg40.71
Total atoms total_atoms9099
Residues n_residues1178
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 dmax153.3
Rg (real space) rg_real41.37
Rg uncertainty (real space) rg_real_error2.00
I(0) (real space) i0_real2.5670e+08
I(0) uncertainty (real space) i0_real_error5.1480e+06
Rg (reciprocal space) rg_reciprocal40.74
I(0) (reciprocal space) i0_reciprocal256500000.0000
Solution quality estimate total_estimate0.7184
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.4
Skewness Skewness skewness0.825
Kurtosis Kurtosis kurtosis0.244
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha50160000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.404; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.370; Smooth: 0.753

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)