4V3D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Conservation Despite Huge Sequence Diversity Allows Epcr Binding by the Pfemp1 Family Implicated in Severe Childhood Malaria.

Lau, C.K.Y.Turner, L.Jespersen, J.S.Lowe, E.D.Petersen, B.Wang, C.W.Petersen, J.E.V.Lusingu, J.Theander, T.G.Lavstsen, T.Higgins, M.K.

(2015) Cell Host Microbe 17: 118

  • DOI: 10.1016/j.chom.2014.11.007
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The PfEMP1 family of surface proteins is central for Plasmodium falciparum virulence and must retain the ability to bind to host receptors while also diversifying to aid immune evasion. The interaction between CIDRα1 domains of PfEMP1 and endothelial ...

    The PfEMP1 family of surface proteins is central for Plasmodium falciparum virulence and must retain the ability to bind to host receptors while also diversifying to aid immune evasion. The interaction between CIDRα1 domains of PfEMP1 and endothelial protein C receptor (EPCR) is associated with severe childhood malaria. We combine crystal structures of CIDRα1:EPCR complexes with analysis of 885 CIDRα1 sequences, showing that the EPCR-binding surfaces of CIDRα1 domains are conserved in shape and bonding potential, despite dramatic sequence diversity. Additionally, these domains mimic features of the natural EPCR ligand and can block this ligand interaction. Using peptides corresponding to the EPCR-binding region, antibodies can be purified from individuals in malaria-endemic regions that block EPCR binding of diverse CIDRα1 variants. This highlights the extent to which such a surface protein family can diversify while maintaining ligand-binding capacity and identifies features that should be mimicked in immunogens to prevent EPCR binding.


    Organizational Affiliation

    Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK. Electronic address: matthew.higgins@bioch.ox.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HB3VAR03 CIDRA DOMAIN
A, C
251Plasmodium falciparum HB3Mutation(s): 0 
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ENDOTHELIAL PROTEIN C RECEPTOR
B, D
170Homo sapiensMutation(s): 0 
Gene Names: PROCREPCR
Find proteins for Q9UNN8 (Homo sapiens)
Go to UniProtKB:  Q9UNN8
NIH Common Fund Data Resources
PHAROS  Q9UNN8
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTY
Query on PTY

Download CCD File 
B, D
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
B, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
B, D
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.13α = 90
b = 94.67β = 90
c = 290.7γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references
  • Version 1.2: 2015-01-28
    Changes: Database references