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- EMDB-22324: Cryo-EM structure of P. falciparum VAR2CSA FCR3 core at 4 A -

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Basic information

Entry
Database: EMDB / ID: EMD-22324
TitleCryo-EM structure of P. falciparum VAR2CSA FCR3 core at 4 A
Map data
Sample
  • Complex: VAR2CSA FCR3
    • Protein or peptide: Erythrocyte membrane protein 1Red blood cell
Function / homology
Function and homology information


host cell surface receptor binding / membrane
Similarity search - Function
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
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsMa R / Tolia NH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1 ZIA AI001237 United States
CitationJournal: Nat Microbiol / Year: 2021
Title: Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA.
Authors: Rui Ma / Tengfei Lian / Rick Huang / Jonathan P Renn / Jennifer D Petersen / Joshua Zimmerberg / Patrick E Duffy / Niraj H Tolia /
Abstract: Plasmodium falciparum VAR2CSA binds to chondroitin sulfate A (CSA) on the surface of the syncytiotrophoblast during placental malaria. This interaction facilitates placental sequestration of malaria ...Plasmodium falciparum VAR2CSA binds to chondroitin sulfate A (CSA) on the surface of the syncytiotrophoblast during placental malaria. This interaction facilitates placental sequestration of malaria parasites resulting in severe health outcomes for both the mother and her offspring. Furthermore, CSA is presented by diverse cancer cells and specific targeting of cells by VAR2CSA may become a viable approach for cancer treatment. In the present study, we determined the cryo-electron microscopy structures of the full-length ectodomain of VAR2CSA from P. falciparum strain NF54 in complex with CSA, and VAR2CSA from a second P. falciparum strain FCR3. The architecture of VAR2CSA is composed of a stable core flanked by a flexible arm. CSA traverses the core domain by binding within two channels and CSA binding does not induce major conformational changes in VAR2CSA. The CSA-binding elements are conserved across VAR2CSA variants and are flanked by polymorphic segments, suggesting immune selection outside the CSA-binding sites. This work provides paths for developing interventions against placental malaria and cancer.
History
DepositionJul 19, 2020-
Header (metadata) releaseJan 13, 2021-
Map releaseJan 13, 2021-
UpdateMar 10, 2021-
Current statusMar 10, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.18
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.18
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jge
  • Surface level: 2.18
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7jge
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22324.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.058 Å
Density
Contour LevelBy AUTHOR: 2.18 / Movie #1: 2.18
Minimum - Maximum-69.432816 - 64.98346
Average (Standard dev.)-8.427394e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.848 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0581.0581.058
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z270.848270.848270.848
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-69.43364.983-0.000

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Supplemental data

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Sample components

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Entire : VAR2CSA FCR3

EntireName: VAR2CSA FCR3
Components
  • Complex: VAR2CSA FCR3
    • Protein or peptide: Erythrocyte membrane protein 1Red blood cell

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Supramolecule #1: VAR2CSA FCR3

SupramoleculeName: VAR2CSA FCR3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Erythrocyte membrane protein 1

MacromoleculeName: Erythrocyte membrane protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 308.823188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGMDSTSTIA NKIEEYLGAK SDDSKIDELL KADPSEVEYY RSGGDGDYLK NNICKITVNH SDSGKYDPCE KKLPPYDDND QWKCQQNSS DGSGKPENIC VPPRRERLCT YNLENLKFDK IRDNNAFLAD VLLTARNEGE KIVQNHPDTN SSNVCNALER S FADLADII ...String:
TGMDSTSTIA NKIEEYLGAK SDDSKIDELL KADPSEVEYY RSGGDGDYLK NNICKITVNH SDSGKYDPCE KKLPPYDDND QWKCQQNSS DGSGKPENIC VPPRRERLCT YNLENLKFDK IRDNNAFLAD VLLTARNEGE KIVQNHPDTN SSNVCNALER S FADLADII RGTDQWKGTN SNLEKNLKQM FAKIRENDKV LQDKYPKDQK YTKLREAWWN ANRQKVWEVI TCGARSNDLL IK RGWRTSG KSDRKKNFEL CRKCGHYEKE VPTKLDYVPQ FLRWLTEWIE DFYREKQNLI DDMERHREEC TREDHKSKEG TSY CSTCKD KCKKYCECVK KWKTEWENQE NKYKDLYEQN KNKTSQKNTS RYDDYVKDFF EKLEANYSSL ENYIKGDPYF AEYA TKLSF ILNPSDANNP SGETANHNDE ACNCNESGIS SVGQAQTSGP SSNKTCITHS SIKTNKKKEC KDVKLGVREN DKDLK ICVI EDTSLSGVDN CCCQDLLGIL QENCSDNKRG SSSNDSCDNK NQDECQKKLE KVFASLTNGY KCDKCKSGTS RSKKKW IWK KSSGNEEGLQ EEYANTIGLP PRTQSLYLGN LPKLENVCED VKDINFDTKE KFLAGCLIVS FHEGKNLKKR YPQNKNS GN KENLCKALEY SFADYGDLIK GTSIWDNEYT KDLELNLQNN FGKLFGKYIK KNNTAEQDTS YSSLDELRES WWNTNKKY I WTAMKHGAEM NITTCNADGS VTGSGSSCDD IPTIDLIPQY LRFLQEWVEN FCEQRQAKVK DVITNCKSCK ESGNKCKTE CKTKCKDECE KYKKFIEACG TAGGGIGTAG SPWSKRWDQI YKRYSKHIED AKRNRKAGTK NCGTSSTTNA AASTDENKCV QSDIDSFFK HLIDIGLTTP SSYLSNVLDD NICGADKAPW TTYTTYTTTE KCNKERDKSK SQSSDTLVVV NVPSPLGNTP Y RYKYACQC KIPTNEETCD DRKEYMNQWS CGSARTMKRG YKNDNYELCK YNGVDVKPTT VRSNSSKLDG NDVTFFNLFE QW NKEIQYQ IEQYMTNANI SCIDEKEVLD SVSDEGTPKV RGGYEDGRNN NTDQGTNCKE KCKCYKLWIE KINDQWGKQK DNY NKFRSK QIYDANKGSQ NKKVVSLSNF LFFSCWEEYI QKYFNGDWSK IKNIGSDTFE FLIKKCGNNS AHGEEIFNEK LKNA EKKCK ENESTDTNIN KSETSCDLNA TNYIRGCQSK TYDGKIFPGK GGEKQWICKD TIIHGDTNGA CIPPRTQNLC VGELW DKSY GGRSNIKNDT KELLKEKIKN AIHKETELLY EYHDTGTAII SKNDKKGQKG KNDPNGLPKG FCHAVQRSFI DYKNMI LGT SVNIYEHIGK LQEDIKKIIE KGTPQQKDKI GGVGSSTENV NAWWKGIERE MWDAVRCAIT KINKKNNNSI FNGDECG VS PPTGNDEDQS VSWFKEWGEQ FCIERLRYEQ NIREACTING KNEKKCINSK SGQGDKIQGA CKRKCEKYKK YISEKKQE W DKQKTKYENK YVGKSASDLL KENYPECISA NFDFIFNDNI EYKTYYPYGD YSSICSCEQV KYYKYNNAEK KNNKSLCYE KDNDMTWSKK YIKKLENGRS LEGVYVPPRR QQLCLYELFP IIIKNEEGME KAKEELLETL QIVAEREAYY LWKQYNPTGK GIDDANKKA CCAIRGSFYD LEDIIKGNDL VHDEYTKYID SKLNEIFGSS DTNDIDTKRA RTDWWENETI TNGTDRKTIR Q LVWDAMQS GVRYAVEEKN ENFPLCMGVE HIGIAKPQFI RWLEEWTNEF CEKYTKYFED MKSKCDPPKR ADTCGDNSNI EC KKACANY TNWLNPKRIE WNGMSNYYNK IYRKSNKESE GGKDYSMIMA PTVIDYLNKR CHGEINGNYI CCSCKNIGAY NTT SGTVNK KLQKKETECE EEKGPLDLMN EVLNKMDKKY SAHKMKCTEV YLEHVEEQLN EIDNAIKDYK LYPLDRCFDD QTKM KVCDL IADAIGCKDK TKLDELDEWN DMDLRGTYNK HKGVLIPPRR RQLCFSRIVR GPANLRSLNE FKEEILKGAQ SEGKF LGNY YKEHKDKEKA LEAMKNSFYD YEDIIKGTDM LTNIEFKDIK IKLDRLLEKE TNNTKKAEDW WKTNKKSIWN AMLCGY KKS GNKIIDPSWC TIPTTETPPQ FLRWIKEWGT NVCIQKQEHK EYVKSKCSNV TNLGAQASES NNCTSEIKKY QEWSRKR SI RWETISKRYK KYKRMDILKD VKEPDANTYL REHCSKCPCG FNDMEEMNNN EDNEKEAFKQ IKEQVKIPAE LEDVIYRI K HHEYDKGNDY ICNKYKNIHD RMKKNNGNFV TDNFVKKSWE ISNGVLIPPR RKNLFLYIDP SKICEYKKDP KLFKDFIYW SAFTEVERLK KAYGGARAKV VHAMKYSFTD IGSIIKGDDM MEKNSSDKIG KILGDTDGQN EKRKKWWDMN KYHIWESMLC GYREAEGDT ETNENCRFPD IESVPQFLRW FQEWSENFCD RRQKLYDKLN SECISAECTN GSVDNSKCTH ACVNYKNYIL T KKTEYEIQ TNKYDNEFKN KNSNDKDAPD YLKEKCNDNK CECLNKHIDD KNKTWKNPYE TLEDTFKSKC DCPKPLPSPI KP DDLPPQA DEPFGTKHHH HHH

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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: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 71.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 271442

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