7rbt

cryo-EM structure of human Gastric inhibitory polypeptide receptor GIPR bound to tirzepatide

Method: ELECTRON MICROSCOPY Dmax: 155.7 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 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 26–380 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Single-chain variable fragment 16 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) nanobody 35 × 1 Tirzepatide × 1 Gastric inhibitory polypeptide receptor × 1 (P48546) 41Y 2-fluoro-4-[(1R)-6-methoxy-1-methyl-2-{(1S)-1-[4-(propan-2-yl)phenyl]ethyl}-1,2,3,4-tetrahydroisoquinolin-5-yl]-6-[(2-methylpropyl)amino]phenol × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.08 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 19–373; UniProt 26–380

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 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) 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) Single-chain variable fragment 16 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) nanobody 35 × 1 Tirzepatide × 1 Gastric inhibitory polypeptide receptor × 1 (P48546) 41Y 2-fluoro-4-[(1R)-6-methoxy-1-methyl-2-{(1S)-1-[4-(propan-2-yl)phenyl]ethyl}-1,2,3,4-tetrahydroisoquinolin-5-yl]-6-[(2-methylpropyl)amino]phenol × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.08 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 12–350; 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 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) 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) Single-chain variable fragment 16 × 1 nanobody 35 × 1 Tirzepatide × 1 Gastric inhibitory polypeptide receptor × 1 (P48546) 41Y 2-fluoro-4-[(1R)-6-methoxy-1-methyl-2-{(1S)-1-[4-(propan-2-yl)phenyl]ethyl}-1,2,3,4-tetrahydroisoquinolin-5-yl]-6-[(2-methylpropyl)amino]phenol × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.08 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 4
Chains and sequence ranges Author chain G; PDBConstruct 1–71; UniProt 1–71

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain R; UniProt 22–466 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) Single-chain variable fragment 16 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) nanobody 35 × 1 Tirzepatide × 1 41Y 2-fluoro-4-[(1R)-6-methoxy-1-methyl-2-{(1S)-1-[4-(propan-2-yl)phenyl]ethyl}-1,2,3,4-tetrahydroisoquinolin-5-yl]-6-[(2-methylpropyl)amino]phenol × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.08 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
PDB entities 7
Chains and sequence ranges Author chain R; PDBConstruct 19–463; UniProt 22–466

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 7rbt

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7rbt
Deposition date deposition_date2021-07-06
Structure title titlecryo-EM structure of human Gastric inhibitory polypeptide receptor GIPR bound to tirzepatide
Keywords keywordsClass B GPCR, glucagon-like peptide-1 receptor, G protein nucleotide exchange factor., MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier43.83
Radius of gyration Rg (electron density) rg_electron43.85
Forward intensity I(0) i0357048000.00
Molecular weight molecular_weight154530.0 kDa
Excluded volume excluded_volume193260 ų
Envelope volume envelope_volume258920 ų
Hydration-shell volume shell_volume52536 ų
Envelope diameter envelope_diameter163.9
Shell Rg shell_rg44.90
Envelope Rg envelope_rg44.33
Shape Rg shape_rg43.86
Total Rg total_rg43.86
Total atoms total_atoms10881
Residues n_residues1384
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 dmax155.7
Rg (real space) rg_real44.26
Rg uncertainty (real space) rg_real_error1.78
I(0) (real space) i0_real3.5700e+08
I(0) uncertainty (real space) i0_real_error6.8580e+06
Rg (reciprocal space) rg_reciprocal43.83
I(0) (reciprocal space) i0_reciprocal356900000.0000
Solution quality estimate total_estimate0.8186
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.3
Skewness Skewness skewness0.580
Kurtosis Kurtosis kurtosis-0.141
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37450000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.739; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.758; Smooth: 0.662

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_id7rbtB01
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_id7rbtR01
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)