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- EMDB-31504: VAR2CSA-CSA 3D7 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-31504
TitleVAR2CSA-CSA 3D7
Map data
Sample
  • Complex: VAR2CSA and CSA
    • Protein or peptide: Erythrocyte membrane protein 1, PfEMP1
KeywordsPlasmodium falciparum / Complex / CSA binding / CELL ADHESION
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang L / Wang Z
Funding support China, 1 items
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, 2021-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31504.png

Downloads & links

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Map

FileDownload / File: emd_31504.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 324 pix.
= 338.256 Å		1.04 Å/pix.
x 324 pix.
= 338.256 Å		1.04 Å/pix.
x 324 pix.
= 338.256 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.044 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.036454096 - 0.20276953
Average (Standard dev.)0.00024048254 (±0.002610567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 338.256 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : VAR2CSA and CSA

EntireName: VAR2CSA and CSA
Components
  • Complex: VAR2CSA and CSA
    • Protein or peptide: Erythrocyte membrane protein 1, PfEMP1

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Supramolecule #1: VAR2CSA and CSA

SupramoleculeName: VAR2CSA and CSA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 306 kDa/nm

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Macromolecule #1: Erythrocyte membrane protein 1, PfEMP1

MacromoleculeName: Erythrocyte membrane protein 1, PfEMP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7
Molecular weightTheoretical: 306.190219 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDKSSIANKI EAYLGAKSDD SKIDQSLKAD PSEVQYYGSG GDGYYLRKNI CKITVNHSDS GTNDPCDRIP PPYGDNDQWK CAIILSKVS EKPENVFVPP RRQRMCINNL EKLNVDKIRD KHAFLADVLL TARNEGERIV QNHPDTNSSN VCNALERSFA D IADIIRGT ...String:
MDKSSIANKI EAYLGAKSDD SKIDQSLKAD PSEVQYYGSG GDGYYLRKNI CKITVNHSDS GTNDPCDRIP PPYGDNDQWK CAIILSKVS EKPENVFVPP RRQRMCINNL EKLNVDKIRD KHAFLADVLL TARNEGERIV QNHPDTNSSN VCNALERSFA D IADIIRGT DLWKGTNSNL EQNLKQMFAK IRENDKVLQD KYPKDQNYRK LREDWWNANR QKVWEVITCG ARSNDLLIKR GW RTSGKSN GDNKLELCRK CGHYEEKVPT KLDYVPQFLR WLTEWIEDFY REKQNLIDDM ERHREECTSE DHKSKEGTSY CST CKDKCK KYCECVKKWK SEWENQKNKY TELYQQNKNE TSQKNTSRYD DYVKDFFKKL EANYSSLENY IKGDPYFAEY ATKL SFILN SSDANNPSEK IQKNNDEVCN CNESGIASVE QEQISDPSSN KTCITHSSIK ANKKKVCKHV KLGVRENDKD LRVCV IEHT SLSGVENCCC QDFLRILQEN CSDNKSGSSS NGSCNNKNQE ACEKNLEKVL ASLTNCYKCD KCKSEQSKKN NKNWIW KKS SGKEGGLQKE YANTIGLPPR TQSLCLVVCL DEKGKKTQEL KNIRTNSELL KEWIIAAFHE GKNLKPSHEK KNDDNGK KL CKALEYSFAD YGDLIKGTSI WDNEYTKDLE LNLQKIFGKL FRKYIKKNNT AEQDTSYSSL DELRESWWNT NKKYIWLA M KHGAGMNSTT CCGDGSVTGS GSSCDDIPTI DLIPQYLRFL QEWVEHFCKQ RQEKVKPVIE NCKSCKESGG TCNGECKTE CKNKCEVYKK FIEDCKGGDG TAGSSWVKRW DQIYKRYSKY IEDAKRNRKA GTKNCGPSST TNAAENKCVQ SDIDSFFKHL IDIGLTTPS SYLSIVLDDN ICGADKAPWT TYTTYTTTEK CNKETDKSKL QQCNTAVVVN VPSPLGNTPH GYKYACQCKI P TNEETCDD RKEYMNQWSC GSARTMKRGY KNDNYELCKY NGVDVKPTTV RSNSSKLDDK DVTFFNLFEQ WNKEIQYQIE QY MTNTKIS CNNEKNVLSR VSDEAAQPKF SDNERDRNSI THEDKNCKEK CKCYSLWIEK INDQWDKQKD NYNKFQRKQI YDA NKGSQN KKVVSLSNFL FFSCWEEYIQ KYFNGDWSKI KNIGSDTFEF LIKKCGNDSG DGETIFSEKL NNAEKKCKEN ESTN NKMKS SETSCDCSEP IYIRGCQPKI YDGKIFPGKG GEKQWICKDT IIHGDTNGAC IPPRTQNLCV GELWDKRYGG RSNIK NDTK ESLKQKIKNA IQKETELLYE YHDKGTAIIS RNPMKGQKEK EEKNNDSNGL PKGFCHAVQR SFIDYKNMIL GTSVNI YEY IGKLQEDIKK IIEKGTTKQN GKTVGSGAEN VNAWWKGIEG EMWDAVRCAI TKINKKQKKN GTFSIDECGI FPPTGND ED QSVSWFKEWS EQFCIERLQY EKNIRDACTN NGQGDKIQGD CKRKCEEYKK YISEKKQEWD KQKTKYENKY VGKSASDL L KENYPECISA NFDFIFNDNI EYKTYYPYGD YSSICSCEQV KYYEYNNAEK KNNKSLCHEK GNDRTWSKKY IKKLENGRT LEGVYVPPRR QQLCLYELFP IIIKNKNDIT NAKKELLETL QIVAEREAYY LWKQYHAHND TTYLAHKKAC CAIRGSFYDL EDIIKGNDL VHDEYTKYID SKLNEIFDSS NKNDIETKRA RTDWWENEAI AVPNITGANK SDPKTIRQLV WDAMQSGVRK A IDEEKEKK KPNENFPPCM GVQHIGIAKP QFIRWLEEWT NEFCEKYTKY FEDMKSNCNL RKGADDCDDN SNIECKKACA NY TNWLNPK RIEWNGMSNY YNKIYRKSNK ESEDGKDYSM IMEPTVIDYL NKRCNGEING NYICCSCKNI GENSTSGTVN KKL QKKETQ CEDNKGPLDL MNKVLNKMDP KYSEHKMKCT EVYLEHVEEQ LKEIDNAIKD YKLYPLDRCF DDKSKMKVCD LIGD AIGCK HKTKLDELDE WNDVDMRDPY NKYKGVLIPP RRRQLCFSRI VRGPANLRNL KEFKEEILKG AQSEGKFLGN YYNED KDKE KALEAMKNSF YDYEYIIKGS DMLTNIQFKD IKRKLDRLLE KETNNTEKVD DWWETNKKSI WNAMLCGYKK SGNKII DPS WCTIPTTETP PQFLRWIKEW GTNVCIQKEE HKEYVKSKCS NVTNLGAQES ESKNCTSEIK KYQEWSRKRS IQWEAIS EG YKKYKGMDEF KNTFKNIKEP DANEPNANEY LKKHCSKCPC GFNDMQEITK YTNIGNEAFK QIKEQVDIPA ELEDVIYR L KHHEYDKGND YICNKYKNIN VNMKKNNDDT WTDLVKNSSD INKGVLLPPR RKNLFLKIDE SDICKYKRDP KLFKDFIYS SAISEVERLK KVYGEAKTKV VHAMKYSFAD IGSIIKGDDM MENNSSDKIG KILGDGVGQN EKRKKWWDMN KYHIWESMLC GYKHAYGNI SENDRKMLDI PNNDDEHQFL RWFQEWTENF CTKRNELYEN MVTACNSAKC NTSNGSVDKK ECTEACKNYS N FILIKKKE YQSLNSQYDM NYKETKAEKK ESPEYFKDKC NGECSCLSEY FKDETRWKNP YETLDDTEVK NN

UniProtKB: Erythrocyte membrane protein 1, PfEMP1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 241954
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

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

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