› 4v3d

X-ray diffraction
2.65Å resolution

The CIDRa domain from HB3var03 PfEMP1 bound to endothelial protein C receptor

Released:
DOI: 10.2210/pdb4v3d/pdb
PDB entry 4v3d coloured by chain, front view.
PDB entry 4v3d coloured by chain, side view.
PDB entry 4v3d coloured by chain, top view.
Source organisms:
Primary publication:
Structural conservation despite huge sequence diversity allows EPCR binding by the PfEMP1 family implicated in severe childhood malaria.
Lau CK, Turner L, Jespersen JS, Lowe ED, Petersen B, Wang CW, Petersen JE, Lusingu J, Theander TG, Lavstsen T, Higgins MK
Cell Host Microbe 17 118-29 (2015)
PMID: 25482433

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-165254 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
HB3VAR03 CIDRA DOMAIN Chains: A, C
Molecule details ›
Chains: A, C
Length: 251 amino acids
Theoretical weight: 29.46 KDa
Source organism: Plasmodium falciparum HB3
Expression system: Escherichia coli B
Endothelial protein C receptor Chains: B, D
Molecule details ›
Chains: B, D
Length: 170 amino acids
Theoretical weight: 19.7 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: Q9UNN8 (Residues: 25-194; Coverage: 77%)
Gene names: EPCR, PROCR
Sequence domains: MHC-I family domain
Structure domains: MHC class I-like antigen recognition-like

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
2 bound ligands:
Ligand PTY 2 x PTY
Ligand NAG 3 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: C2221
Unit cell:
a: 66.13Å b: 94.67Å c: 290.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.224 0.222 0.255
Expression systems:
  • Escherichia coli B
  • Drosophila melanogaster

Quick links

Citations

21 review citations

Variant surface antigens of Plasmodium falciparum and their roles in severe malaria.
Wahlgren et al. (2017)
20 more

1 mention without citation

Structure-Guided Design of a Synthetic Mimic of an Endothelial Protein C Receptor-Binding PfEMP1 Protein.
Barber et al. (2021)