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- PDB-7fap: Structure of VAR2CSA-CSA 3D7 -

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Basic information

Entry
Database: PDB / ID: 7fap
TitleStructure of VAR2CSA-CSA 3D7
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 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang, L. / Wang, Z.
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 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erythrocyte membrane protein 1, PfEMP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,9652
Polymers306,1901
Non-polymers2,7741
Water00
1


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

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Components

#1: Protein Erythrocyte membrane protein 1, PfEMP1


Mass: 306190.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1200600 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I639
#2: Polysaccharide 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-2- ...2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 2774.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAc[4S]b1-3DGlcpAb1-3DGalpNAc[4S]b1-4DGlcpAb1-3DGalpNAc[4S]b1-4DGlcpAb1-3DGalpNAc[4S]b1-4DGlcpAb1-3DGalpNAc[4S]b1-4DGlcpAb1-3DGalpNAc[4S]b1-4DGlcpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,12,11/[a2122A-1b_1-5][a2112h-1b_1-5_2*NCC/3=O_4*OSO/3=O/3=O]/1-2-1-2-1-2-1-2-1-2-1-2/a4-b1_b3-c1_c4-d1_d3-e1_e4-f1_f3-g1_g4-h1_h3-i1_i4-j1_j3-k1_k3-l1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpA]{[(4+1)][b-D-GalpNAc4SO3]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GalpNAc4SO3]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GalpNAc4SO3]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GalpNAc4SO3]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GalpNAc4SO3]{[(3+1)][b-D-4-deoxy-GlcpA]{[(3+1)][b-D-GalpNAc4SO3]{}}}}}}}}}}}}LINUCSPDB-CARE
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: VAR2CSA and CSA / Type: COMPLEX / Entity ID: #1 / 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 / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 241954 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410417
ELECTRON MICROSCOPYf_angle_d0.59313970
ELECTRON MICROSCOPYf_dihedral_angle_d5.1971281
ELECTRON MICROSCOPYf_chiral_restr0.0421476
ELECTRON MICROSCOPYf_plane_restr0.0041742

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