› 6ruv

X-ray diffraction
6.15Å resolution

Structure of the SCIN stabilized C3bBb convertase bound to Properdin and a the non-inhibitory nanobody hFPNb1

Released:
DOI: 10.2210/pdb6ruv/pdb
PDB entry 6ruv coloured by chain, front view.
PDB entry 6ruv coloured by chain, side view.
PDB entry 6ruv coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System.
Pedersen DV, Gadeberg TAF, Thomas C, Wang Y, Joram N, Jensen RK, Mazarakis SMM, Revel M, El Sissy C, Petersen SV, Lindorff-Larsen K, Thiel S, Laursen NS, Fremeaux-Bacchi V, Andersen GR
Front Immunol 10 2007 (2019)
PMID: 31507604

Function and Biology Details

Reaction catalysed: 
Cleavage of Arg-|-Ser bond in complement component C3 alpha-chain to yield C3a and C3b, and Arg-|- bond in complement component C5 alpha-chain to yield C5a and C5b.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
PDBe Complex ID:
PDB-CPX-208315 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (10 distinct):
Nanobody hFPNb1 Chains: R, S
Molecule details ›
Chains: R, S
Length: 131 amino acids
Theoretical weight: 14.52 KDa
Source organism: Lama glama
Expression system: Escherichia coli
Properdin Chains: U, X
Molecule details ›
Chains: U, X
Length: 170 amino acids
Theoretical weight: 18.64 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P27918 (Residues: 28-191; Coverage: 37%)
Gene names: CFP, PFC
Sequence domains:
Properdin Chains: V, Y
Molecule details ›
Chains: V, Y
Length: 221 amino acids
Theoretical weight: 24.72 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P27918 (Residues: 256-469; Coverage: 48%)
Gene names: CFP, PFC
Sequence domains: Thrombospondin type 1 domain
Complement C3 beta chain Chains: A, G
Molecule details ›
Chains: A, G
Length: 645 amino acids
Theoretical weight: 71.39 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P01024 (Residues: 23-667; Coverage: 39%)
Gene names: C3, CPAMD1
Sequence domains:
Complement C3b alpha' chain Chains: B, H
Molecule details ›
Chains: B, H
Length: 915 amino acids
Theoretical weight: 104.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P01024 (Residues: 749-1663; Coverage: 56%)
Gene names: C3, CPAMD1
Sequence domains:
Complement factor B Bb fragment Chains: J, L
Molecule details ›
Chains: J, L
Length: 505 amino acids
Theoretical weight: 57.04 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P00751 (Residues: 260-764; Coverage: 68%)
Gene names: BF, BFD, CFB
Sequence domains:
Staphylococcal complement inhibitor Chains: N, Q
Molecule details ›
Chains: N, Q
Length: 86 amino acids
Theoretical weight: 9.88 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q931M7 (Residues: 31-116; Coverage: 100%)
Gene names: SAV1942, scn
Sequence domains: Staphylococcal complement inhibitor SCIN

Ligands and Environments

Carbohydrate polymer : NEW Components: FUC, BGC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: FUC, NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand MAN 21 x MAN
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: P212121
Unit cell:
a: 123.99Å b: 354.03Å c: 367.84Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.244 0.242 0.271
Expression systems:
  • Escherichia coli
  • Homo sapiens

Quick links

Citations

7 review citations

Meta-heterogeneity: Evaluating and Describing the Diversity in Glycosylation Between Sites on the Same Glycoprotein.
Čaval et al. (2021)
6 more

1 mention without citation

Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System.
Pedersen et al. (2019)