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- EMDB-31505: VAR2CSA 3D7 ectodomain core region -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-31505
TitleVAR2CSA 3D7 ectodomain core region
Map data
Sample
  • Complex: VAR2CSA
    • Protein or peptide: Erythrocyte membrane protein 1, PfEMP1
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) / Plasmodium falciparum (isolate 3D7) (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang L / Zhaoning W
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) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7fas
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31505.png

Downloads & links

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Map

FileDownload / File: emd_31505.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 / Movie #1: 0.025
Minimum - Maximum-0.05593301 - 0.1717581
Average (Standard dev.)0.0009501658 (±0.0024294734)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0441.0441.044
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z338.256338.256338.256
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS324324324
D min/max/mean-0.0560.1720.001

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Supplemental data

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Sample components

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Entire : VAR2CSA

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

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Supramolecule #1: VAR2CSA

SupramoleculeName: VAR2CSA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 (isolate 3D7) (eukaryote) / Strain: isolate 3D7
Molecular weightTheoretical: 228.991188 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 Y

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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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 304160
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-7fas:
VAR2CSA 3D7 ectodomain core region

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