› 6ysq

X-ray diffraction
3.3Å resolution

The hC4Nb8 complement inhibitory nanobody in complex with C4b

Released:
DOI: 10.2210/pdb6ysq/pdb
PDB entry 6ysq coloured by chain, front view.
PDB entry 6ysq coloured by chain, side view.
PDB entry 6ysq coloured by chain, top view.
Source organisms:
Primary publication:
An Ultrahigh-Affinity Complement C4b-Specific Nanobody Inhibits In Vivo Assembly of the Classical Pathway Proconvertase.
Zarantonello A, Presumey J, Simoni L, Yalcin E, Fox R, Hansen A, Olesen HG, Thiel S, Johnson MB, Stevens B, Laursen NS, Carroll MC, Andersen GR
J Immunol 205 1678-1694 (2020)
PMID: 32769120

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-209601 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Complement C4 beta chain Chains: A, B
Molecule details ›
Chains: A, B
Length: 656 amino acids
Theoretical weight: 71.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P0C0L5 (Residues: 20-675; Coverage: 38%)
Gene names: C4B, C4B_2, CO4, CPAMD3
Sequence domains:
C4b-A Chains: C, D
Molecule details ›
Chains: C, D
Length: 690 amino acids
Theoretical weight: 75.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P0C0L4 (Residues: 757-1446; Coverage: 40%)
Gene names: C4A, CO4, CPAMD2
Sequence domains:
Complement C4 gamma chain Chains: E, F
Molecule details ›
Chains: E, F
Length: 291 amino acids
Theoretical weight: 33.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P0C0L5 (Residues: 1454-1744; Coverage: 17%)
Gene names: C4B, C4B_2, CO4, CPAMD3
Sequence domains:
hC4Nb8 nanobody Chains: G, H
Molecule details ›
Chains: G, H
Length: 132 amino acids
Theoretical weight: 14.68 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: P21
Unit cell:
a: 131.2Å b: 89.51Å c: 231.2Å
α: 90° β: 97.552° γ: 90°
R-values:
R R work R free
0.222 0.221 0.272
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Nanobodies: new avenue to treat kidney disease.
Wanner et al. (2021)
4 other articles

1 mention without citation

Nanobodies Provide Insight into the Molecular Mechanisms of the Complement Cascade and Offer New Therapeutic Strategies.
Zarantonello et al. (2021)