7B54 | pdb_00007b54

VAR2CSA full ectodomain in present of plCS, DBL1-DBL4

• PDB DOI: https://doi.org/10.2210/pdb7B54/pdb
• EM Map EMD-12018: EMDB EMDataResource

• Classification: CELL ADHESION
• Organism(s): Plasmodium falciparum
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2020-12-03 Released: 2021-06-02 
• Deposition Author(s): Wang, K.T., Dagil, R., Gourdon, P.E., Salanti, A.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM reveals the architecture of placental malaria VAR2CSA and provides molecular insight into chondroitin sulfate binding.

Wang, K., Dagil, R., Lavstsen, T., Misra, S.K., Spliid, C.B., Wang, Y., Gustavsson, T., Sandoval, D.R., Vidal-Calvo, E.E., Choudhary, S., Agerbaek, M.O., Lindorff-Larsen, K., Nielsen, M.A., Theander, T.G., Sharp, J.S., Clausen, T.M., Gourdon, P., Salanti, A.

(2021) Nat Commun 12: 2956-2956

• PubMed: 34011972 
• DOI: https://doi.org/10.1038/s41467-021-23254-1
• Primary Citation Related Structures: 
  7B52, 7B54, 7NNH


• PubMed Abstract: 
  

  Placental malaria can have severe consequences for both mother and child and effective vaccines are lacking. Parasite-infected red blood cells sequester in the placenta through interaction between parasite-expressed protein VAR2CSA and the glycosaminoglycan chondroitin sulfate A (CS) abundantly present in the intervillous space. Here, we report cryo-EM structures of the VAR2CSA ectodomain at up to 3.1 Å resolution revealing an overall V-shaped architecture and a complex domain organization. Notably, the surface displays a single significantly electropositive patch, compatible with binding of negatively charged CS. Using molecular docking and molecular dynamics simulations as well as comparative hydroxyl radical protein foot-printing of VAR2CSA in complex with placental CS, we identify the CS-binding groove, intersecting with the positively charged patch of the central VAR2CSA structure. We identify distinctive conserved structural features upholding the macro-molecular domain complex and CS binding capacity of VAR2CSA as well as divergent elements possibly allowing immune escape at or near the CS binding site. These observations will support rational design of second-generation placental malaria vaccines.

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Organizational Affiliation: 
• Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, Copenhagen, Denmark.
Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, USA.
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science,Department of Biology, University of Copenhagen, Copenhagen, Denmark.
VAR2Pharmaceuticals, Ole Maaloesvej 3, Copenhagen, Denmark.
Department of Chemistry and Biochemistry, University of Mississippi, Oxford, MS, USA.
Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark. [e-mail].
Department of Experimental Medical Science, Lund University, Lund, Sweden. [e-mail].
Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, Copenhagen, Denmark. [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: 219.44 kDa 
• Atom Count: 14,148 
• Modeled Residue Count: 1,732 
• Deposited Residue Count: 1,895 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VAR2CSA in presence of plCS, DBl1-DBL4,Erythrocyte membrane protein 1	A [auth X]	1,895	Plasmodium falciparum	Mutation(s): 0
UniProt
Find proteins for Q6UDW7 (Plasmodium falciparum) Explore Q6UDW7  Go to UniProtKB:  Q6UDW7

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-02 
Deposition Author(s): Wang, K.T., Dagil, R., Gourdon, P.E., Salanti, A.

Revision History  

• Version 1.0: 2021-06-02
  Type: Initial release
  
• Version 1.1: 2022-05-25
  Changes: Database references, Structure summary
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary