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


This is version 2.1 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: 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 ...

    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

    Centre for Medical Parasitology, Department of Immunology and Microbiology (ISIM), Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), 2100 Copenhagen, Denmark. Electronic address: atrj@sund.ku.dk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Erythrocyte membrane protein 1 (PfEMP1) A488Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF11_0521PF3D7_1150400
Find proteins for Q8IHM0 (Plasmodium falciparum (isolate 3D7))
Explore Q8IHM0 
Go to UniProtKB:  Q8IHM0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Intercellular adhesion molecule 1 B186Homo sapiensMutation(s): 0 
Gene Names: ICAM1
Find proteins for P05362 (Homo sapiens)
Explore P05362 
Go to UniProtKB:  P05362
NIH Common Fund Data Resources
PHAROS:  P05362
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download Ideal Coordinates CCD File 
B
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
3PO
Query on 3PO

Download Ideal Coordinates CCD File 
A
TRIPHOSPHATE
H5 O10 P3
UNXRWKVEANCORM-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
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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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