5MZA

The DBLb domain of PF11_0521 PfEMP1 bound to human ICAM-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Structure-Guided Identification of a Family of Dual Receptor-Binding PfEMP1 that Is Associated with Cerebral Malaria.

Lennartz, F.Adams, Y.Bengtsson, A.Olsen, R.W.Turner, L.Ndam, N.T.Ecklu-Mensah, G.Moussiliou, A.Ofori, M.F.Gamain, B.Lusingu, J.P.Petersen, J.E.Wang, C.W.Nunes-Silva, S.Jespersen, J.S.Lau, C.K.Theander, T.G.Lavstsen, T.Hviid, L.Higgins, M.K.Jensen, A.T.

(2017) Cell Host Microbe 21: 403-414

  • DOI: https://doi.org/10.1016/j.chom.2017.02.009
  • Primary Citation of Related Structures:  
    5MZA

  • PubMed Abstract: 

    Cerebral malaria is a deadly outcome of infection by Plasmodium falciparum, occurring when parasite-infected erythrocytes accumulate in the brain. These erythrocytes display parasite proteins of the PfEMP1 family that bind various endothelial receptors. Despite the importance of cerebral malaria, a binding phenotype linked to its symptoms has not been identified. Here, we used structural biology to determine how a group of PfEMP1 proteins interacts with intercellular adhesion molecule 1 (ICAM-1), allowing us to predict binders from a specific sequence motif alone. Analysis of multiple Plasmodium falciparum genomes showed that ICAM-1-binding PfEMP1s also interact with endothelial protein C receptor (EPCR), allowing infected erythrocytes to synergistically bind both receptors. Expression of these PfEMP1s, predicted to bind both ICAM-1 and EPCR, is associated with increased risk of developing cerebral malaria. This study therefore reveals an important PfEMP1-binding phenotype that could be targeted as part of a strategy to prevent cerebral malaria.


  • Organizational Affiliation

    Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Erythrocyte membrane protein 1 (PfEMP1)488Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF11_0521PF3D7_1150400
UniProt
Find proteins for Q8IHM0 (Plasmodium falciparum (isolate 3D7))
Explore Q8IHM0 
Go to UniProtKB:  Q8IHM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IHM0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Intercellular adhesion molecule 1186Homo sapiensMutation(s): 0 
Gene Names: ICAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P05362 (Homo sapiens)
Explore P05362 
Go to UniProtKB:  P05362
PHAROS:  P05362
GTEx:  ENSG00000090339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05362
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P05362-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.639α = 90
b = 109.83β = 90
c = 112.83γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom101020/Z/13/Z

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-10-07
    Changes: Structure summary
  • Version 2.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary