+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31504 | |||||||||
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Title | Structure of VAR2CSA-CSA 3D7 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information modulation by symbiont 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 | |||||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Wang L / Wang Z | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31504.map.gz | 3.8 MB | EMDB map data format | |
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Header (meta data) | emd-31504-v30.xml emd-31504.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | emd_31504.png | 50 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31504 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31504 | HTTPS FTP |
-Related structure data
Related structure data | 7fapMC 7fasC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31504.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.044 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : VAR2CSA and CSA
Entire | Name: VAR2CSA and CSA |
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Components |
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-Supramolecule #1: VAR2CSA and CSA
Supramolecule | Name: VAR2CSA and CSA / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Molecular weight | Theoretical: 306 kDa/nm |
-Macromolecule #1: Erythrocyte membrane protein 1, PfEMP1
Macromolecule | Name: Erythrocyte membrane protein 1, PfEMP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 |
Molecular weight | Theoretical: 306.190219 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
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Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 241954 |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7fap: |