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- EMDB-22327: Cryo-EM structure of P. falciparum VAR2CSA NF54 core in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-22327
TitleCryo-EM structure of P. falciparum VAR2CSA NF54 core in complex with CSA at 3.36 A
Map data
Sample
  • Complex: VAR2CSA NF54 core in complex with CSA
    • Protein or peptide: Erythrocyte membrane protein 1
  • Ligand: 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose
KeywordsPlacental malaria / VAR2CSA / Duffy binding domain / CSA / PfEMP1 / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


host cell surface receptor binding / 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 / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain
Similarity search - Domain/homology
Erythrocyte membrane protein 1
Similarity search - Component
Biological speciesPlasmodium falciparum (isolate NF54) (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.96
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.96
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jgh
  • Surface level: 3.96
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22327.png

Downloads & links

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Map

FileDownload / File: emd_22327.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 300 pix.
= 317.4 Å		1.06 Å/pix.
x 300 pix.
= 317.4 Å		1.06 Å/pix.
x 300 pix.
= 317.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.96 / Movie #1: 3.96
Minimum - Maximum-34.588287000000001 - 55.298859999999998
Average (Standard dev.)-0.000000000000906 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0581.0581.058
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z317.400317.400317.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-34.58855.299-0.000

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Supplemental data

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Sample components

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Entire : VAR2CSA NF54 core in complex with CSA

EntireName: VAR2CSA NF54 core in complex with CSA
Components
  • Complex: VAR2CSA NF54 core in complex with CSA
    • Protein or peptide: Erythrocyte membrane protein 1
  • Ligand: 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose

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Supramolecule #1: VAR2CSA NF54 core in complex with CSA

SupramoleculeName: VAR2CSA NF54 core in complex with CSA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Plasmodium falciparum (isolate NF54) (eukaryote) / Strain: isolate NF54

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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 (isolate NF54) (eukaryote) / Strain: isolate NF54
Molecular weightTheoretical: 308.706031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGMDKSSIAN KIEAYLGAKS DDSKIDQSLK ADPSEVQYYG SGGDGYYLRK NICKITVNHS DSGTNDPCDR IPPPYGDNDQ WKCAIILSK VSEKPENVFV PPRRQRMCIN NLEKLNVDKI RDKHAFLADV LLTARNEGER IVQNHPDTNS SNVCNALERS F ADIADIIR ...String:
TGMDKSSIAN KIEAYLGAKS DDSKIDQSLK ADPSEVQYYG SGGDGYYLRK NICKITVNHS DSGTNDPCDR IPPPYGDNDQ WKCAIILSK VSEKPENVFV PPRRQRMCIN NLEKLNVDKI RDKHAFLADV LLTARNEGER IVQNHPDTNS SNVCNALERS F ADIADIIR GTDLWKGTNS NLEQNLKQMF AKIRENDKVL QDKYPKDQNY RKLREDWWNA NRQKVWEVIT CGARSNDLLI KR GWRTSGK SNGDNKLELC RKCGHYEEKV PTKLDYVPQF LRWLTEWIED FYREKQNLID DMERHREECT SEDHKSKEGT SYC STCKDK CKKYCECVKK WKSEWENQKN KYTELYQQNK NETSQKNTSR YDDYVKDFFK KLEANYSSLE NYIKGDPYFA EYAT KLSFI LNSSDANNPS EKIQKNNDEV CNCNESGIAS VEQEQISDPS SNKTCITHSS IKANKKKVCK HVKLGVREND KDLRV CVIE HTSLSGVENC CCQDFLRILQ ENCSDNKSGS SSNGSCNNKN QEACEKNLEK VLASLTNCYK CDKCKSEQSK KNNKNW IWK KSSGKEGGLQ KEYANTIGLP PRTQSLCLVV CLDEKGKKTQ ELKNIRTNSE LLKEWIIAAF HEGKNLKPSH EKKNDDN GK KLCKALEYSF ADYGDLIKGT SIWDNEYTKD LELNLQKIFG KLFRKYIKKN NTAEQDTSYS SLDELRESWW NTNKKYIW L AMKHGAGMNS TTCCGDGSVT GSGSSCDDIP TIDLIPQYLR FLQEWVEHFC KQRQEKVKPV IENCKSCKES GGTCNGECK TECKNKCEVY KKFIEDCKGG DGTAGSSWVK RWDQIYKRYS KYIEDAKRNR KAGTKNCGPS STTNAAENKC VQSDIDSFFK HLIDIGLTT PSSYLSIVLD DNICGADKAP WTTYTTYTTT EKCNKETDKS KLQQCNTAVV VNVPSPLGNT PHGYKYACQC K IPTNEETC DDRKEYMNQW SCGSARTMKR GYKNDNYELC KYNGVDVKPT TVRSNSSKLD DKDVTFFNLF EQWNKEIQYQ IE QYMTNTK ISCNNEKNVL SRVSDEAAQP KFSDNERDRN SITHEDKNCK EKCKCYSLWI EKINDQWDKQ KDNYNKFQRK QIY DANKGS QNKKVVSLSN FLFFSCWEEY IQKYFNGDWS KIKNIGSDTF EFLIKKCGND SGDGETIFSE KLNNAEKKCK ENES TNNKM KSSETSCDCS EPIYIRGCQP KIYDGKIFPG KGGEKQWICK DTIIHGDTNG ACIPPRTQNL CVGELWDKRY GGRSN IKND TKESLKQKIK NAIQKETELL YEYHDKGTAI ISRNPMKGQK EKEEKNNDSN GLPKGFCHAV QRSFIDYKNM ILGTSV NIY EYIGKLQEDI KKIIEKGTTK QNGKTVGSGA ENVNAWWKGI EGEMWDAVRC AITKINKKQK KNGTFSIDEC GIFPPTG ND EDQSVSWFKE WSEQFCIERL QYEKNIRDAC TNNGQGDKIQ GDCKRKCEEY KKYISEKKQE WDKQKTKYEN KYVGKSAS D LLKENYPECI SANFDFIFND NIEYKTYYPY GDYSSICSCE QVKYYEYNNA EKKNNKSLCH EKGNDRTWSK KYIKKLENG RTLEGVYVPP RRQQLCLYEL FPIIIKNKND ITNAKKELLE TLQIVAEREA YYLWKQYHAH NDTTYLAHKK ACCAIRGSFY DLEDIIKGN DLVHDEYTKY IDSKLNEIFD SSNKNDIETK RARTDWWENE AIAVPNITGA NKSDPKTIRQ LVWDAMQSGV R KAIDEEKE KKKPNENFPP CMGVQHIGIA KPQFIRWLEE WTNEFCEKYT KYFEDMKSNC NLRKGADDCD DNSNIECKKA CA NYTNWLN PKRIEWNGMS NYYNKIYRKS NKESEDGKDY SMIMEPTVID YLNKRCNGEI NGNYICCSCK NIGENSTSGT VNK KLQKKE TQCEDNKGPL DLMNKVLNKM DPKYSEHKMK CTEVYLEHVE EQLKEIDNAI KDYKLYPLDR CFDDKSKMKV CDLI GDAIG CKHKTKLDEL DEWNDVDMRD PYNKYKGVLI PPRRRQLCFS RIVRGPANLR NLKEFKEEIL KGAQSEGKFL GNYYN EDKD KEKALEAMKN SFYDYEYIIK GSDMLTNIQF KDIKRKLDRL LEKETNNTEK VDDWWETNKK SIWNAMLCGY KKSGNK IID PSWCTIPTTE TPPQFLRWIK EWGTNVCIQK EEHKEYVKSK CSNVTNLGAQ ESESKNCTSE IKKYQEWSRK RSIQWEA IS EGYKKYKGMD EFKNTFKNIK EPDANEPNAN EYLKKHCSKC PCGFNDMQEI TKYTNIGNEA FKQIKEQVDI PAELEDVI Y RLKHHEYDKG NDYICNKYKN INVNMKKNND DTWTDLVKNS SDINKGVLLP PRRKNLFLKI DESDICKYKR DPKLFKDFI YSSAISEVER LKKVYGEAKT KVVHAMKYSF ADIGSIIKGD DMMENNSSDK IGKILGDGVG QNEKRKKWWD MNKYHIWESM LCGYKHAYG NISENDRKML DIPNNDDEHQ FLRWFQEWTE NFCTKRNELY ENMVTACNSA KCNTSNGSVD KKECTEACKN Y SNFILIKK KEYQSLNSQY DMNYKETKAE KKESPEYFKD KCNGECSCLS EYFKDETRWK NPYETLDDTE VKNNCMCKPP PP ASNNGTK HHHHHH

UniProtKB: Erythrocyte membrane protein 1

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Macromolecule #3: 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose

MacromoleculeName: 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose / type: ligand / ID: 3 / Number of copies: 1 / Formula: ASG
Molecular weightTheoretical: 301.271 Da
Chemical component information

ChemComp-ASG:
2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 299571
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION

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