3CPZ

Crystal structure of VAR2CSA DBL3x domain in the presence of dodecasaccharide of CSA

• PDB DOI: https://doi.org/10.2210/pdb3CPZ/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-01 Released: 2008-09-02 
• Deposition Author(s): Singh, K., Gittis, A.G., Nguyen, P., Gowda, D.C., Miller, L.H., Garboczi, D.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.353 
• R-Value Work: 0.299 
• R-Value Observed: 0.299 

Starting Model: experimental

Literature

Structure of the DBL3x domain of pregnancy-associated malaria protein VAR2CSA complexed with chondroitin sulfate A.

Singh, K., Gittis, A.G., Nguyen, P., Gowda, D.C., Miller, L.H., Garboczi, D.N.

(2008) Nat Struct Mol Biol 15: 932-938

• PubMed: 19172746 
• DOI: https://doi.org/10.1038/nsmb.1479
• Primary Citation of Related Structures:  
  3CML, 3CPZ


• PubMed Abstract: 
  

  Plasmodium falciparum-infected erythrocytes bind to chondroitin sulfate A (CSA) in the placenta via the VAR2CSA protein, a member of the P. falciparum erythrocyte membrane protein-1 family, leading to life-threatening malaria in pregnant women with severe effects on their fetuses and newborns. Here we describe the structure of the CSA binding DBL3x domain, a Duffy binding-like (DBL) domain of VAR2CSA. By forming a complex of DBL3x with CSA oligosaccharides and determining its structure, we have identified the CSA binding site to be a cluster of conserved positively charged residues on subdomain 2 and subdomain 3. Mutation or chemical modification of lysine residues at the site markedly diminished CSA binding to DBL3x. The location of the CSA binding site is an important step forward in the molecular understanding of pregnancy-associated malaria and offers a new target for vaccine development.

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Organizational Affiliation: 

Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, Maryland 20852, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.56 kDa 
• Atom Count: 2,247 
• Modelled Residue Count: 297 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Erythrocyte membrane protein 1	A	362	Plasmodium falciparum	Mutation(s): 0  Gene Names: var
UniProt
Find proteins for Q6UDW7 (Plasmodium falciparum) Explore Q6UDW7  Go to UniProtKB:  Q6UDW7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.353 
• R-Value Work: 0.299 
• R-Value Observed: 0.299 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.52	α = 90
b = 86.76	β = 90
c = 101.57	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Singh, K., Gittis, A.G., Nguyen, P., Gowda, D.C., Miller, L.H., Garboczi, D.N.

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Refinement description