8GZN

IgM-var2CSA complex

• PDB DOI: https://doi.org/10.2210/pdb8GZN/pdb
• EM Map EMD-34399: EMDB EMDataResource

• Classification: CELL ADHESION/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Plasmodium falciparum
• Expression System: Drosophila
• Mutation(s): No 


• Deposited: 2022-09-27 Released: 2023-10-25 
• Deposition Author(s): Akhouri, R.R., Goel, S., Skoglund, U.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-electron microscopy of IgM-VAR2CSA complex reveals IgM inhibits binding of Plasmodium falciparum to Chondroitin Sulfate A.

Akhouri, R.R., Goel, S., Skoglund, U.

(2023) Nat Commun 14: 6391-6391

• PubMed: 37828011 
• DOI: https://doi.org/10.1038/s41467-023-41838-x
• Primary Citation of Related Structures:  
  8GZN


• PubMed Abstract: 
  

  Placental malaria is caused by Plasmodium falciparum-infected erythrocytes (IEs) adhering to chondroitin sulfate proteoglycans in placenta via VAR2CSA-type PfEMP1. Human pentameric immunoglobulin M (IgM) binds to several types of PfEMP1, including VAR2CSA via its Fc domain. Here, a 3.6 Å cryo-electron microscopy map of the IgM-VAR2CSA complex reveals that two molecules of VAR2CSA bind to the Cµ4 of IgM through their DBL3X and DBL5ε domains. The clockwise and anti-clockwise rotation of the two VAR2CSA molecules on opposite faces of IgM juxtaposes C-termini of both VAR2CSA near the J chain, where IgM creates a wall between both VAR2CSA molecules and hinders its interaction with its receptor. To support this, we show when VAR2CSA is bound to IgM, its staining on IEs as well as binding of IEs to chondroitin sulfate A in vitro is severely compromised.

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Organizational Affiliation: 

Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 13-mer - A8B2C2D1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 8-mer - A8 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 1,132.41 kDa 
• Atom Count: 35,322 
• Modelled Residue Count: 4,400 
• Deposited Residue Count: 10,026 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin heavy constant mu	A, B, C, D, E, F, G, H, K, L	453	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01871 (Homo sapiens) Explore P01871  Go to UniProtKB:  P01871
PHAROS:  P01871 GTEx:  ENSG00000211899

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Erythrocyte membrane protein 1	I, M	2,680	Plasmodium falciparum	Mutation(s): 0  Gene Names: var
UniProt
Find proteins for Q6UDW7 (Plasmodium falciparum) Explore Q6UDW7  Go to UniProtKB:  Q6UDW7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin J chain	J	136	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01591 (Homo sapiens) Explore P01591  Go to UniProtKB:  P01591
PHAROS:  P01591 GTEx:  ENSG00000132465

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-25 
Deposition Author(s): Akhouri, R.R., Goel, S., Skoglund, U.

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Funding Organization	Location	Grant Number
Other government	Japan	core grant

Revision History  

• Version 1.0: 2023-10-25
  Type: Initial release