8hqc

Structure of a GPCR-G protein in complex with a natural peptide agonist

Method: ELECTRON MICROSCOPY Dmax: 137.4 Å Quality: GOOD

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

C5a anaphylatoxin chemotactic receptor 1

Mus musculus

UniProt P30993

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 2–351 Not recorded Guanine nucleotide-binding protein G(o) subunit alpha × 1 (P09471) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) C5a anaphylatoxin × 1 (P01031) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Antibody fragment × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.89 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.

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C5AR1_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 58–407; UniProt 2–351

Guanine nucleotide-binding protein G(o) subunit alpha

Homo sapiens

UniProt P09471

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 4–57 Chain B; UniProt 182–354 Mutation:G42D,E43N,A227D,G230D,I332A,V335I C5a anaphylatoxin chemotactic receptor 1 × 1 (P30993) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) C5a anaphylatoxin × 1 (P01031) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Antibody fragment × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.89 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.

83 other PDB entries and 83 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAO_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 16–69; UniProt 4–57 Author chain B; PDBConstruct 78–240; UniProt 182–354

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 2–340 Not recorded C5a anaphylatoxin chemotactic receptor 1 × 1 (P30993) Guanine nucleotide-binding protein G(o) subunit alpha × 1 (P09471) C5a anaphylatoxin × 1 (P01031) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Antibody fragment × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.89 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 3
Chains and sequence ranges Author chain C; PDBConstruct 12–350; UniProt 2–340

C5a anaphylatoxin

Homo sapiens

UniProt P01031

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 D; UniProt 678–751 Not recorded C5a anaphylatoxin chemotactic receptor 1 × 1 (P30993) Guanine nucleotide-binding protein G(o) subunit alpha × 1 (P09471) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Antibody fragment × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.89 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 63 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CO5_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–74; UniProt 678–751

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded C5a anaphylatoxin chemotactic receptor 1 × 1 (P30993) Guanine nucleotide-binding protein G(o) subunit alpha × 1 (P09471) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) C5a anaphylatoxin × 1 (P01031) Antibody fragment × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.89 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 5
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 8hqc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8hqc
Deposition date deposition_date2022-12-13
Structure title titleStructure of a GPCR-G protein in complex with a natural peptide agonist
Keywords keywordsGPCR, G protein, SIGNALING PROTEIN, SIGNALING PROTEIN-IMMUNE SYSTEM complex; SIGNALING PROTEIN/IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier40.61
Radius of gyration Rg (electron density) rg_electron40.41
Forward intensity I(0) i0225745000.00
Molecular weight molecular_weight121360.0 kDa
Excluded volume excluded_volume151620 ų
Envelope volume envelope_volume214510 ų
Hydration-shell volume shell_volume46207 ų
Envelope diameter envelope_diameter148.6
Shell Rg shell_rg43.11
Envelope Rg envelope_rg40.88
Shape Rg shape_rg40.36
Total Rg total_rg40.75
Total atoms total_atoms8538
Residues n_residues1186
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 dmax137.4
Rg (real space) rg_real40.74
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real2.2570e+08
I(0) uncertainty (real space) i0_real_error4.0740e+06
Rg (reciprocal space) rg_reciprocal40.61
I(0) (reciprocal space) i0_reciprocal225700000.0000
Solution quality estimate total_estimate0.8656
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.3
Skewness Skewness skewness0.397
Kurtosis Kurtosis kurtosis-0.353
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28490000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.871; Smooth: 0.752

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (2)

9. Files and Curves (10)