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4p3a

Crystal structure of the mouse C5a anaphylatoxin

Method: X-RAY DIFFRACTION Dmax: 81.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Complement C5

Mus musculus

UniProt P06684

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 679–755 Fragment：UNP residues 679-755 FMT FORMIC ACID × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.7；277 K；0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15 Resolution 1.40 Å R-free 0.174
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 679–755 Fragment：UNP residues 679-755 FMT FORMIC ACID × 7 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.7；277 K；0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15 Resolution 1.40 Å R-free 0.174
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 679–755 Fragment：UNP residues 679-755 FMT FORMIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.7；277 K；0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15 Resolution 1.40 Å R-free 0.174
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 679–755 Fragment：UNP residues 679-755 FMT FORMIC ACID × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.7；277 K；0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15 Resolution 1.40 Å R-free 0.174
5 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 679–755 Chain B； UniProt 679–755 Fragment：UNP residues 679-755 FMT FORMIC ACID × 10 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.7；277 K；0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15 Resolution 1.40 Å R-free 0.174
6 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 679–755 Chain D； UniProt 679–755 Fragment：UNP residues 679-755 FMT FORMIC ACID × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.7；277 K；0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15 Resolution 1.40 Å R-free 0.174

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.

Other PDB Difference from Current Entry 4P3A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4P3B Crystal structure of the mouse C5a-desArg anaphylatoxin Deposited 2014-03-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 679–754（76 aa） Fragment：UNP residues 679-754
Not recorded FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.3；277 K；0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate
Resolution 2.10 Å R-free 0.224
4P3B Crystal structure of the mouse C5a-desArg anaphylatoxin Deposited 2014-03-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 679–754（76 aa） Fragment：UNP residues 679-754
Not recorded FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.3；277 K；0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate
Resolution 2.10 Å R-free 0.224
4P3B Crystal structure of the mouse C5a-desArg anaphylatoxin Deposited 2014-03-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 679–754（76 aa） Fragment：UNP residues 679-754
Not recorded FMT FORMIC ACID × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.3；277 K；0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate
Resolution 2.10 Å R-free 0.224
4P3B Crystal structure of the mouse C5a-desArg anaphylatoxin Deposited 2014-03-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 679–754（76 aa） Fragment：UNP residues 679-754
Not recorded FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.3；277 K；0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate
Resolution 2.10 Å R-free 0.224
4P3B Crystal structure of the mouse C5a-desArg anaphylatoxin Deposited 2014-03-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 679–754（76 aa） Fragment：UNP residues 679-754
Chain C 679–754（76 aa） Fragment：UNP residues 679-754
Not recorded FMT FORMIC ACID × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.3；277 K；0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate
Resolution 2.10 Å R-free 0.224
4P3B Crystal structure of the mouse C5a-desArg anaphylatoxin Deposited 2014-03-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 679–754（76 aa） Fragment：UNP residues 679-754
Chain D 679–754（76 aa） Fragment：UNP residues 679-754
Not recorded FMT FORMIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.3；277 K；0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate
Resolution 2.10 Å R-free 0.224
4WB2 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a complement anaphylatoxin Deposited 2014-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 679–755（77 aa）
Not recorded ACT ACETATE ION × 2 CA CALCIUM ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.2 M NaCl, 0.1 M Na cacodylate pH 6.0, 8% (w/v) PEG 8000
Resolution 1.80 Å R-free 0.193
4WB2 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a complement anaphylatoxin Deposited 2014-09-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 679–755（77 aa）
Not recorded ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.2 M NaCl, 0.1 M Na cacodylate pH 6.0, 8% (w/v) PEG 8000
Resolution 1.80 Å R-free 0.193
4WB2 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a complement anaphylatoxin Deposited 2014-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain C 679–755（77 aa）
Not recorded ACT ACETATE ION × 2 CA CALCIUM ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.2 M NaCl, 0.1 M Na cacodylate pH 6.0, 8% (w/v) PEG 8000
Resolution 1.80 Å R-free 0.193
4WB3 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin Deposited 2014-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 679–754（76 aa）
Not recorded CA CALCIUM ION × 3 ACT ACETATE ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；0.2 M ammonium acetate, 0.1 M Na acetate pH 4.0, 15% (w/v) PEG 4000
Resolution 2.00 Å R-free 0.199
4WB3 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin Deposited 2014-09-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 679–754（76 aa）
Not recorded ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；0.2 M ammonium acetate, 0.1 M Na acetate pH 4.0, 15% (w/v) PEG 4000
Resolution 2.00 Å R-free 0.199
4WB3 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin Deposited 2014-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain C 679–754（76 aa）
Not recorded CA CALCIUM ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；0.2 M ammonium acetate, 0.1 M Na acetate pH 4.0, 15% (w/v) PEG 4000
Resolution 2.00 Å R-free 0.199
8JZP Structure of mouse C5a-human C5aR1-Go complex Deposited 2023-07-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 679–755（77 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
9KWG Structure of mouse C5a bound mouse C5aR1 in complex with Go Deposited 2024-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 679–755（77 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
9KWX Structure of mouse C5a-desArg bound mouse C5aR1 in complex with Go Deposited 2024-12-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 679–754（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å

6 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CO5_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–79； UniProt 679–755 Author chain B； PDBConstruct 3–79； UniProt 679–755 Author chain C； PDBConstruct 3–79； UniProt 679–755 Author chain D； PDBConstruct 3–79； UniProt 679–755

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 4p3a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4p3a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4p3a
Deposition date deposition_date2014-03-06
Structure title titleCrystal structure of the mouse C5a anaphylatoxin
Keywords keywordscomplement anaphylatoxin, C5a, four-helix bundle, GPCR agonist, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.34 Å
Radius of gyration Rg (electron density) rg_electron25.08 Å
Forward intensity I(0) i019619400.00
Molecular weight molecular_weight32466.0 kDa
Excluded volume excluded_volume40133 ų
Envelope volume envelope_volume52879 ų
Hydration-shell volume shell_volume18515 ų
Envelope diameter envelope_diameter82.7 Å
Shell Rg shell_rg30.84 Å
Envelope Rg envelope_rg25.10 Å
Shape Rg shape_rg25.09 Å
Total Rg total_rg25.73 Å
Total atoms total_atoms2260
Residues n_residues276
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax81.8 Å
Rg (real space) rg_real25.50 Å
Rg uncertainty (real space) rg_real_error0.94 Å
I(0) (real space) i0_real1.9620e+07
I(0) uncertainty (real space) i0_real_error3.2010e+05
Rg (reciprocal space) rg_reciprocal25.45 Å
I(0) (reciprocal space) i0_reciprocal19620000.0000
Solution quality estimate total_estimate0.8503
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.8 Å
Skewness Skewness skewness0.349
Kurtosis Kurtosis kurtosis-0.741
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2079000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.827; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.592; Smooth: 0.978
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd4p3aa1
Class classa — All alpha proteins
Fold Fold folda.50 — Anaphylotoxins (complement system)
Superfamily Superfamily superfamilya.50.1 — Anaphylotoxins (complement system)
Family Family familya.50.1.1 — Anaphylotoxins (complement system)
Domain ID domain_idd4p3aa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4p3ab1
Class classa — All alpha proteins
Fold Fold folda.50 — Anaphylotoxins (complement system)
Superfamily Superfamily superfamilya.50.1 — Anaphylotoxins (complement system)
Family Family familya.50.1.1 — Anaphylotoxins (complement system)
Domain ID domain_idd4p3ab2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4p3ac1
Class classa — All alpha proteins
Fold Fold folda.50 — Anaphylotoxins (complement system)
Superfamily Superfamily superfamilya.50.1 — Anaphylotoxins (complement system)
Family Family familya.50.1.1 — Anaphylotoxins (complement system)
Domain ID domain_idd4p3ac2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4p3ad1
Class classa — All alpha proteins
Fold Fold folda.50 — Anaphylotoxins (complement system)
Superfamily Superfamily superfamilya.50.1 — Anaphylotoxins (complement system)
Family Family familya.50.1.1 — Anaphylotoxins (complement system)
Domain ID domain_idd4p3ad2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id4p3aA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily20 — Anaphylotoxins (complement system)
Domain ID domain_id4p3aB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily20 — Anaphylotoxins (complement system)
Domain ID domain_id4p3aC00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily20 — Anaphylotoxins (complement system)
Domain ID domain_id4p3aD00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily20 — Anaphylotoxins (complement system)
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8. Citations (1)

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9. Files and Curves (10)