7eib

Cryo-EM structure of the type 1 bradykinin receptor in complex with the des-Arg10-kallidin and an Gq protein

Method: ELECTRON MICROSCOPY Dmax: 116.7 Å Quality: GOOD

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

B1 bradykinin receptor

Homo sapiens

UniProt P46663

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 2–350 Mutation:F126W LYS-ARG-PRO-PRO-GLY-PHE-SER-PRO-PHE × 1 G subunit q (Gi1-Gq chimeric) × 1 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) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BKRB1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 107–455; UniProt 2–350

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 C; UniProt 2–340 Not recorded B1 bradykinin receptor × 1 (P46663) LYS-ARG-PRO-PRO-GLY-PHE-SER-PRO-PHE × 1 G subunit q (Gi1-Gq chimeric) × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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 C; 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 1–71 Not recorded B1 bradykinin receptor × 1 (P46663) LYS-ARG-PRO-PRO-GLY-PHE-SER-PRO-PHE × 1 G subunit q (Gi1-Gq chimeric) × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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 E; 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 7eib

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7eib
Deposition date deposition_date2021-03-30
Structure title titleCryo-EM structure of the type 1 bradykinin receptor in complex with the des-Arg10-kallidin and an Gq protein
Keywords keywordsBradykinin receptors, Kinin, GPCR, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier34.32
Radius of gyration Rg (electron density) rg_electron34.34
Forward intensity I(0) i0155635000.00
Molecular weight molecular_weight102100.0 kDa
Excluded volume excluded_volume128590 ų
Envelope volume envelope_volume163090 ų
Hydration-shell volume shell_volume41056 ų
Envelope diameter envelope_diameter121.7
Shell Rg shell_rg39.21
Envelope Rg envelope_rg34.42
Shape Rg shape_rg34.38
Total Rg total_rg34.56
Total atoms total_atoms7204
Residues n_residues928
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 dmax116.7
Rg (real space) rg_real34.45
Rg uncertainty (real space) rg_real_error0.89
I(0) (real space) i0_real1.5560e+08
I(0) uncertainty (real space) i0_real_error2.3370e+06
Rg (reciprocal space) rg_reciprocal34.37
I(0) (reciprocal space) i0_reciprocal155600000.0000
Solution quality estimate total_estimate0.8692
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.5
Skewness Skewness skewness0.436
Kurtosis Kurtosis kurtosis-0.348
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41630000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.825

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7eibC01
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)