8itm

Cryo-EM structure of GIPR splice variant 2 (SV2) in complex with Gs protein

Method: ELECTRON MICROSCOPY Dmax: 111.3 Å Quality: REASONABLE

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

Gastric inhibitory polypeptide receptor

Homo sapiens

UniProt P48546

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 58–385 Mutation:T284F 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 3.13 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 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GIPR_HUMAN
Isoform P48546-3
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 33–360; UniProt 58–385

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–394 Mutation:S54N,G226A,E268A,N271K,K274D,R280K,T284D,I285T Gastric inhibitory polypeptide receptor × 1 (P48546) 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 3.13 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 2
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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Gastric inhibitory polypeptide receptor × 1 (P48546) 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 3.13 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 3
Chains and sequence ranges Author chain B; PDBConstruct 7–345; 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Gastric inhibitory polypeptide receptor × 1 (P48546) 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 3.13 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 4
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 8itm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8itm
Deposition date deposition_date2023-03-22
Structure title titleCryo-EM structure of GIPR splice variant 2 (SV2) in complex with Gs protein
Keywords keywordsCryo-electron microscopy; G protein-coupled receptor; splice variant; receptor activation., STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier34.19
Radius of gyration Rg (electron density) rg_electron34.01
Forward intensity I(0) i0199077000.00
Molecular weight molecular_weight112330.0 kDa
Excluded volume excluded_volume140320 ų
Envelope volume envelope_volume185700 ų
Hydration-shell volume shell_volume45964 ų
Envelope diameter envelope_diameter119.6
Shell Rg shell_rg40.02
Envelope Rg envelope_rg34.27
Shape Rg shape_rg34.01
Total Rg total_rg34.47
Total atoms total_atoms7905
Residues n_residues1035
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 dmax111.3
Rg (real space) rg_real34.26
Rg uncertainty (real space) rg_real_error1.00
I(0) (real space) i0_real1.9910e+08
I(0) uncertainty (real space) i0_real_error3.3120e+06
Rg (reciprocal space) rg_reciprocal34.22
I(0) (reciprocal space) i0_reciprocal199100000.0000
Solution quality estimate total_estimate0.6186
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.7
Skewness Skewness skewness0.444
Kurtosis Kurtosis kurtosis-0.204
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha42330000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.872; Stabil: 0.998; Sysdev: 0.122; Positv: 1.000; Valcen: 0.998; Smooth: 0.064

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)