9kx6

Structure of human C5a-desArg bound mouse C5aR1 in complex with Go

Method: ELECTRON MICROSCOPY Dmax: 135.1 Å Quality: GOOD

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

Muscarinic acetylcholine receptor M4,C5a anaphylatoxin chemotactic receptor 1

Mus musculus

UniProt P08173

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 2–23 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) Complement C5 × 1 (P01031) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Antibody fragment ScFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.11 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.

37 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACM4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 26–47; UniProt 2–23

Muscarinic acetylcholine receptor M4,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 Insufficient information 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) Complement C5 × 1 (P01031) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Antibody fragment ScFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.11 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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 6–53 Chain B; UniProt 182–354 Mutation:G42D,E43N,A227D,G230D,I332A,V335I Muscarinic acetylcholine receptor M4,C5a anaphylatoxin chemotactic receptor 1 × 1 (P08173,P30993) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Complement C5 × 1 (P01031) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Antibody fragment ScFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.11 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 18–65; UniProt 6–53 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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 2–340 Not recorded Muscarinic acetylcholine receptor M4,C5a anaphylatoxin chemotactic receptor 1 × 1 (P08173,P30993) Guanine nucleotide-binding protein G(o) subunit alpha × 1 (P09471) Complement C5 × 1 (P01031) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Antibody fragment ScFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.11 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

Complement C5

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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 678–750 Not recorded Muscarinic acetylcholine receptor M4,C5a anaphylatoxin chemotactic receptor 1 × 1 (P08173,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 ScFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.11 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 1–73; UniProt 678–750

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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Muscarinic acetylcholine receptor M4,C5a anaphylatoxin chemotactic receptor 1 × 1 (P08173,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) Complement C5 × 1 (P01031) Antibody fragment ScFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.11 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 9kx6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9kx6
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id9kx6
Deposition date deposition_date2024-12-06
最后修订 last_revision2025-11-26
Structure title titleStructure of human C5a-desArg bound mouse C5aR1 in complex with Go
Keywords keywordsGPCR, G protein, SIGNALING PROTEIN, SIGNALING PROTEIN-IMMUNE SYSTEM complex; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier39.75
Radius of gyration Rg (electron density) rg_electron39.39
Forward intensity I(0) i0227827000.00
Molecular weight molecular_weight122440.0 kDa
Excluded volume excluded_volume153110 ų
Envelope volume envelope_volume206490 ų
Hydration-shell volume shell_volume45233 ų
Envelope diameter envelope_diameter145.1
Shell Rg shell_rg42.68
Envelope Rg envelope_rg40.00
Shape Rg shape_rg39.37
Total Rg total_rg39.68
Total atoms total_atoms8616
Residues n_residues1195
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 dmax135.1
Rg (real space) rg_real39.94
Rg uncertainty (real space) rg_real_error1.35
I(0) (real space) i0_real2.2780e+08
I(0) uncertainty (real space) i0_real_error3.4860e+06
Rg (reciprocal space) rg_reciprocal39.83
I(0) (reciprocal space) i0_reciprocal227800000.0000
Solution quality estimate total_estimate0.8712
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.3
Skewness Skewness skewness0.368
Kurtosis Kurtosis kurtosis-0.411
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30180000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.889; Smooth: 0.814

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)