› 5jpm

X-ray diffraction
3.75Å resolution

Structure of the complex of human complement C4 with MASP-2 rebuilt using iMDFF

Released:
DOI: 10.2210/pdb5jpm/pdb
PDB entry 5jpm coloured by chain, front view.
PDB entry 5jpm coloured by chain, side view.
PDB entry 5jpm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.
Croll TI, Andersen GR
Acta Crystallogr D Struct Biol 72 1006-16 (2016)
PMID: 27599733

Function and Biology Details

Reaction catalysed: 
Selective cleavage after Arg(223) in complement component C2 (-Ser-Leu-Gly-Arg-|-Lys-Ile-Gln-Ile) and after Arg(76) in complement component C4 (-Gly-Leu-Gln-Arg-|-Ala-Leu-Glu-Ile)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126142 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (6 distinct):
Complement C4 beta chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 656 amino acids
Theoretical weight: 71.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P0C0L4 (Residues: 20-675; Coverage: 38%)
Gene names: C4A, CO4, CPAMD2
Sequence domains:
Structure domains:
Complement C4-A alpha chain Chains: B, E
Molecule details ›
Chains: B, E
Length: 767 amino acids
Theoretical weight: 84.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P0C0L4 (Residues: 680-1446; Coverage: 45%)
Gene names: C4A, CO4, CPAMD2
Sequence domains:
Structure domains:
Complement C4 gamma chain Chains: C, F
Molecule details ›
Chains: C, F
Length: 291 amino acids
Theoretical weight: 33.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P0C0L4 (Residues: 1454-1744; Coverage: 17%)
Gene names: C4A, CO4, CPAMD2
Sequence domains:
Structure domains:
Mannan-binding lectin serine protease 2 A chain Chains: G, I
Molecule details ›
Chains: G, I
Length: 154 amino acids
Theoretical weight: 16.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O00187 (Residues: 291-444; Coverage: 23%)
Gene name: MASP2
Sequence domains: Sushi repeat (SCR repeat)
Structure domains: Complement Module, domain 1
Mannan-binding lectin serine protease 2 B chain Chains: H, J
Molecule details ›
Chains: H, J
Length: 242 amino acids
Theoretical weight: 26.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O00187 (Residues: 445-686; Coverage: 36%)
Gene name: MASP2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
No bound ligands
1 modified residue:
Ligand TYS 4 x TYS

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29, SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P21
Unit cell:
a: 99.01Å b: 215.01Å c: 142.86Å
α: 90° β: 110.11° γ: 90°
R-values:
R R work R free
0.213 0.212 0.268
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Plant Proton Pumps and Cytosolic pH-Homeostasis.
Cosse et al. (2021)
2 more

2 mentions without citation

Complement is activated by elevated IgG3 hexameric platforms and deposits C4b onto distinct antibody domains.
Abendstein et al. (2023)
1 more