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- PDB-8c44: HB3VAR03 apo headstructure (PfEMP1 A) complexed with EPCR -

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Basic information

Entry
Database: PDB / ID: 8c44
TitleHB3VAR03 apo headstructure (PfEMP1 A) complexed with EPCR
Components
  • Endothelial protein C receptor
  • PfEMP1
KeywordsCELL ADHESION / Plasmodium falciparum / Cerebral Malaria / PfEMP1 / EPCR
Function / homology
Function and homology information


negative regulation of coagulation / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / blood coagulation / signaling receptor activity / host cell surface receptor binding / focal adhesion / centrosome / perinuclear region of cytoplasm / cell surface ...negative regulation of coagulation / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / blood coagulation / signaling receptor activity / host cell surface receptor binding / focal adhesion / centrosome / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Endothelial protein C receptor / : / PfEMP1 protein, CIDRalpha1 domain / Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment / N-terminal segments of PfEMP1 / : / Cysteine-rich interdomain region 1 gamma / Cysteine-Rich Interdomain Region 1 gamma / Duffy-binding-like domain, C-terminal subdomain / Duffy-binding-like domain ...Endothelial protein C receptor / : / PfEMP1 protein, CIDRalpha1 domain / Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment / N-terminal segments of PfEMP1 / : / Cysteine-rich interdomain region 1 gamma / Cysteine-Rich Interdomain Region 1 gamma / Duffy-binding-like domain, C-terminal subdomain / Duffy-binding-like domain / PFEMP1 DBL domain / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain / MHC-I family domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / PfEMP1 / Endothelial protein C receptor
Similarity search - Component
Biological speciesPlasmodium falciparum HB3 (eukaryote)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRaghavan, S.S.R. / Lavstsen, T. / Wang, K.T.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Danish Council for Independent Research9039-00285A Denmark
LundbeckfondenR344-2020-934 Denmark
CitationJournal: Structure / Year: 2023
Title: Endothelial protein C receptor binding induces conformational changes to severe malaria-associated group A PfEMP1.
Authors: Sai Sundar Rajan Raghavan / Louise Turner / Rasmus W Jensen / Nicolai Tidemand Johansen / Daniel Skjold Jensen / Pontus Gourdon / Jinqiu Zhang / Yong Wang / Thor Grundtvig Theander / Kaituo ...Authors: Sai Sundar Rajan Raghavan / Louise Turner / Rasmus W Jensen / Nicolai Tidemand Johansen / Daniel Skjold Jensen / Pontus Gourdon / Jinqiu Zhang / Yong Wang / Thor Grundtvig Theander / Kaituo Wang / Thomas Lavstsen /
Abstract: Severe Plasmodium falciparum malaria infections are caused by microvascular sequestration of parasites binding to the human endothelial protein C receptor (EPCR) via the multi-domain P. falciparum ...Severe Plasmodium falciparum malaria infections are caused by microvascular sequestration of parasites binding to the human endothelial protein C receptor (EPCR) via the multi-domain P. falciparum erythrocyte membrane protein 1 (PfEMP1) adhesion ligands. Using cryogenic electron microscopy (Cryo-EM) and PfEMP1 sequence diversity analysis, we found that group A PfEMP1 CIDRα1 domains interact with the adjacent DBLα1 domain through central, conserved residues of the EPCR-binding site to adopt a compact conformation. Upon EPCR binding, the DBLα1 domain is displaced, and the EPCR-binding helix of CIDRα1 is turned, kinked, and twisted to reach a rearranged, stable EPCR-bound conformation. The unbound conformation and the required transition to the EPCR-bound conformation may represent a conformational masking mechanism of immune evasion for the PfEMP1 family.
History
DepositionDec 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
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Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
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Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PfEMP1
C: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,5864
Polymers164,6312
Non-polymers9552
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein PfEMP1


Mass: 145158.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum HB3 (eukaryote) / Gene: PFHG_05052 / Production host: Spodoptera frugiperda granulovirus / References: UniProt: A0A0L7KL67
#2: Protein Endothelial protein C receptor / Activated protein C receptor / APC receptor / Endothelial cell protein C receptor


Mass: 19471.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PROCR, EPCR / Production host: Spodoptera frugiperda granulovirus / References: UniProt: Q9UNN8
#3: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Multidomain PFEMP1 A complexed with EPCR / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.175 MDa / Experimental value: YES
Source (natural)Organism: Plasmodium falciparum HB3 (eukaryote)
Source (recombinant)Organism: Spodoptera frugiperda granulovirus
Buffer solutionpH: 7.5
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
2cryoSPARC3.3image acquisition
8PHENIXmodel refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 505000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056056
ELECTRON MICROSCOPYf_angle_d0.6498140
ELECTRON MICROSCOPYf_dihedral_angle_d17.42800
ELECTRON MICROSCOPYf_chiral_restr0.045849
ELECTRON MICROSCOPYf_plane_restr0.0061030

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