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- PDB-7fas: VAR2CSA 3D7 ectodomain core region -

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Basic information

Entry
Database: PDB / ID: 7fas
TitleVAR2CSA 3D7 ectodomain core region
ComponentsErythrocyte membrane protein 1, PfEMP1
KeywordsCELL ADHESION / Plasmodium falciparum / Complex / CSA binding
Function / homology
Function and homology information


symbiont-mediated perturbation of host erythrocyte aggregation / infected host cell surface knob / antigenic variation / adhesion of symbiont to microvasculature / cell adhesion molecule binding / cell-cell adhesion / host cell surface receptor binding / host cell plasma membrane / membrane
Similarity search - Function
Duffy-binding-like domain / PFEMP1 DBL domain / Plasmodium falciparum erythrocyte membrane protein 1, N-terminal / N-terminal segments of P. falciparum erythrocyte membrane protein / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment superfamily / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment / acidic terminal segments, variant surface antigen of PfEMP1 / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain
Similarity search - Domain/homology
Erythrocyte membrane protein 1, PfEMP1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang, L. / Zhaoning, W.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Cell Discov / Year: 2021
Title: The molecular mechanism of cytoadherence to placental or tumor cells through VAR2CSA from Plasmodium falciparum.
Authors: Weiwei Wang / Zhaoning Wang / Xiuna Yang / Yan Gao / Xiang Zhang / Long Cao / Aguang Dai / Jin Sun / Lei Sun / Lubin Jiang / Zhenguo Chen / Lanfeng Wang /
History
DepositionJul 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: Erythrocyte membrane protein 1, PfEMP1


Theoretical massNumber of molelcules
Total (without water)228,9911
Polymers228,9911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area67410 Å2

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Components

#1: Protein Erythrocyte membrane protein 1, PfEMP1


Mass: 228991.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_1200600 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I639
Has ligand of interestN
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: VAR2CSA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 306 kDa/nm / Experimental value: NO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 6.5
SpecimenEmbedding 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
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 304160 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410731
ELECTRON MICROSCOPYf_angle_d0.57714394
ELECTRON MICROSCOPYf_dihedral_angle_d15.51366
ELECTRON MICROSCOPYf_chiral_restr0.0391520
ELECTRON MICROSCOPYf_plane_restr0.0041823

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