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- PDB-8c3y: HB3VAR03 apo headstructure (PfEMP1 A) -

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Basic information

Entry
Database: PDB / ID: 8c3y
TitleHB3VAR03 apo headstructure (PfEMP1 A)
ComponentsPfEMP1Plasmodium falciparum erythrocyte membrane protein 1
KeywordsCELL ADHESION / Plasmodium falciparum / Cerebral Malaria / PfEMP1 / EPCR
Function / homology
Function and homology information


host cell surface receptor binding / membrane
Similarity search - Function
: / 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 / PFEMP1 DBL domain / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum HB3 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PfEMP1


Theoretical massNumber of molelcules
Total (without water)145,1291
Polymers145,1291
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area50380 Å2
MethodPISA

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Components

#1: Protein PfEMP1 / Plasmodium falciparum erythrocyte membrane protein 1


Mass: 145128.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum HB3 (eukaryote) / Gene: PFHG_05052 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0L7KL67

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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 architecture of PfEMP1 A / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.145 MDa / Experimental value: YES
Source (natural)Organism: Plasmodium falciparum HB3 (eukaryote)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 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 FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: cryoSPARC / Version: 3.3 / Category: image acquisition
CTF correctionType: NONE
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 750035 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0118184
ELECTRON MICROSCOPYf_angle_d0.9111007
ELECTRON MICROSCOPYf_dihedral_angle_d14.6683092
ELECTRON MICROSCOPYf_chiral_restr0.0551130
ELECTRON MICROSCOPYf_plane_restr0.0071430

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