8ykd

Cryo-EM structure of ADGRG2-Gs complex with NTF nanobody

Method: ELECTRON MICROSCOPY Dmax: 118.6 Å Quality: GOOD

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

Guanine nucleotide-binding protein G(s) subunit alpha

Spodoptera

UniProt P63091

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 204–394 Mutation:G236A,A259D,S262D,L272D,A366S,I372A,V375I Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Guanine nucleotide-binding protein subunit gamma × 1 (A0A7J7XNR4) Nanobody-35 × 1 Adhesion G-protein coupled receptor G2 × 1 (Q8CJ12) ScFv-16 × 1 AND 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 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 GNAS_CANLF
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 181–361; UniProt 204–394

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

Spodoptera

UniProt P62871

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 Guanine nucleotide-binding protein G(s) subunit alpha × 1 (P63091) Guanine nucleotide-binding protein subunit gamma × 1 (A0A7J7XNR4) Nanobody-35 × 1 Adhesion G-protein coupled receptor G2 × 1 (Q8CJ12) ScFv-16 × 1 AND 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 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.

72 other PDB entries and 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 20–358; UniProt 2–340

Guanine nucleotide-binding protein subunit gamma

Spodoptera

UniProt A0A7J7XNR4

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 19–99 Not recorded Guanine nucleotide-binding protein G(s) subunit alpha × 1 (P63091) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Nanobody-35 × 1 Adhesion G-protein coupled receptor G2 × 1 (Q8CJ12) ScFv-16 × 1 AND 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 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.

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

View Construct and Data Evidence
UniProt name A0A7J7XNR4_RHIFE
Isoform
PDB entities 3
Chains and sequence ranges Author chain G; PDBConstruct 28–108; UniProt 19–99

Adhesion G-protein coupled receptor G2

Spodoptera

UniProt Q8CJ12

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 38–891 Not recorded Guanine nucleotide-binding protein G(s) subunit alpha × 1 (P63091) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Guanine nucleotide-binding protein subunit gamma × 1 (A0A7J7XNR4) Nanobody-35 × 1 ScFv-16 × 1 AND 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 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.

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AGRG2_MOUSE
Isoform
PDB entities 5
Chains and sequence ranges Author chain R; PDBConstruct 25–878; UniProt 38–891

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 8ykd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ykd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ykd
Deposition date deposition_date2024-03-04
Structure title titleCryo-EM structure of ADGRG2-Gs complex with NTF nanobody
Keywords keywordsGPCR, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier36.23
Radius of gyration Rg (electron density) rg_electron36.11
Forward intensity I(0) i0266071000.00
Molecular weight molecular_weight133660.0 kDa
Excluded volume excluded_volume167710 ų
Envelope volume envelope_volume212240 ų
Hydration-shell volume shell_volume49552 ų
Envelope diameter envelope_diameter124.0
Shell Rg shell_rg41.88
Envelope Rg envelope_rg36.16
Shape Rg shape_rg36.10
Total Rg total_rg36.51
Total atoms total_atoms9410
Residues n_residues1225
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 dmax118.6
Rg (real space) rg_real36.19
Rg uncertainty (real space) rg_real_error1.22
I(0) (real space) i0_real2.6610e+08
I(0) uncertainty (real space) i0_real_error4.7590e+06
Rg (reciprocal space) rg_reciprocal36.22
I(0) (reciprocal space) i0_reciprocal266100000.0000
Solution quality estimate total_estimate0.8996
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.1
Skewness Skewness skewness0.256
Kurtosis Kurtosis kurtosis-0.524
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha59340000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.948

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)