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- EMDB-12017: VAR2CSA full ectodomain -

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Basic information

Entry
Database: EMDB / ID: EMD-12017
TitleVAR2CSA full ectodomain
Map data
Sample
  • Complex: VAR2CSA full ectodomain
    • Protein or peptide: Erythrocyte membrane protein 1
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: 3.8 Å
AuthorsWang KT / Gourdon PE / Dagil R / Salanti A
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM reveals the architecture of placental malaria VAR2CSA and provides molecular insight into chondroitin sulfate binding.
Authors: Kaituo Wang / Robert Dagil / Thomas Lavstsen / Sandeep K Misra / Charlotte B Spliid / Yong Wang / Tobias Gustavsson / Daniel R Sandoval / Elena Ethel Vidal-Calvo / Swati Choudhary / Mette Ø ...Authors: Kaituo Wang / Robert Dagil / Thomas Lavstsen / Sandeep K Misra / Charlotte B Spliid / Yong Wang / Tobias Gustavsson / Daniel R Sandoval / Elena Ethel Vidal-Calvo / Swati Choudhary / Mette Ø Agerbaek / Kresten Lindorff-Larsen / Morten A Nielsen / Thor G Theander / Joshua S Sharp / Thomas Mandel Clausen / Pontus Gourdon / Ali Salanti /
Abstract: Placental malaria can have severe consequences for both mother and child and effective vaccines are lacking. Parasite-infected red blood cells sequester in the placenta through interaction between ...Placental malaria can have severe consequences for both mother and child and effective vaccines are lacking. Parasite-infected red blood cells sequester in the placenta through interaction between parasite-expressed protein VAR2CSA and the glycosaminoglycan chondroitin sulfate A (CS) abundantly present in the intervillous space. Here, we report cryo-EM structures of the VAR2CSA ectodomain at up to 3.1 Å resolution revealing an overall V-shaped architecture and a complex domain organization. Notably, the surface displays a single significantly electropositive patch, compatible with binding of negatively charged CS. Using molecular docking and molecular dynamics simulations as well as comparative hydroxyl radical protein foot-printing of VAR2CSA in complex with placental CS, we identify the CS-binding groove, intersecting with the positively charged patch of the central VAR2CSA structure. We identify distinctive conserved structural features upholding the macro-molecular domain complex and CS binding capacity of VAR2CSA as well as divergent elements possibly allowing immune escape at or near the CS binding site. These observations will support rational design of second-generation placental malaria vaccines.
History
DepositionDec 3, 2020-
Header (metadata) releaseApr 21, 2021-
Map releaseApr 21, 2021-
UpdateMay 25, 2022-
Current statusMay 25, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.56
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.56
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b52
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7b52
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12017.png

Downloads & links

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Map

FileDownload / File: emd_12017.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 365.2 Å		0.83 Å/pix.
x 440 pix.
= 365.2 Å		0.83 Å/pix.
x 440 pix.
= 365.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.56 / Movie #1: 0.56
Minimum - Maximum-0.73559713 - 1.8424778
Average (Standard dev.)0.00061450474 (±0.06511752)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 365.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z365.200365.200365.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.7361.8420.001

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Supplemental data

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Sample components

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Entire : VAR2CSA full ectodomain

EntireName: VAR2CSA full ectodomain
Components
  • Complex: VAR2CSA full ectodomain
    • Protein or peptide: Erythrocyte membrane protein 1

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Supramolecule #1: VAR2CSA full ectodomain

SupramoleculeName: VAR2CSA full ectodomain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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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: 307.549812 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDSTSTIANK IEEYLGAKSD DSKIDELLKA DPSEVEYYRS GGDGDYLKNN ICKITVNHSD SGKYDPCEKK LPPYDDNDQW KCQQNSSDG SGKPENICVP PRRERLCTYN LENLKFDKIR DNNAFLADVL LTARNEGEKI VQNHPDTNSS NVCNALERSF A DLADIIRG ...String:
MDSTSTIANK IEEYLGAKSD DSKIDELLKA DPSEVEYYRS GGDGDYLKNN ICKITVNHSD SGKYDPCEKK LPPYDDNDQW KCQQNSSDG SGKPENICVP PRRERLCTYN LENLKFDKIR DNNAFLADVL LTARNEGEKI VQNHPDTNSS NVCNALERSF A DLADIIRG TDQWKGTNSN LEKNLKQMFA KIRENDKVLQ DKYPKDQKYT KLREAWWNAN RQKVWEVITC GARSNDLLIK RG WRTSGKS DRKKNFELCR KCGHYEKEVP TKLDYVPQFL RWLTEWIEDF YREKQNLIDD MERHREECTR EDHKSKEGTS YCS TCKDKC KKYCECVKKW KTEWENQENK YKDLYEQNKN KTSQKNTSRY DDYVKDFFEK LEANYSSLEN YIKGDPYFAE YATK LSFIL NPSDANNPSG ETANHNDEAC NCNESGISSV GQAQTSGPSS NKTCITHSSI KTNKKKECKD VKLGVRENDK DLKIC VIED TSLSGVDNCC CQDLLGILQE NCSDNKRGSS SNDSCDNKNQ DECQKKLEKV FASLTNGYKC DKCKSGTSRS KKKWIW KKS SGNEEGLQEE YANTIGLPPR TQSLYLGNLP KLENVCEDVK DINFDTKEKF LAGCLIVSFH EGKNLKKRYP QNKNSGN KE NLCKALEYSF ADYGDLIKGT SIWDNEYTKD LELNLQNNFG KLFGKYIKKN NTAEQDTSYS SLDELRESWW NTNKKYIW T AMKHGAEMNI TTCNADGSVT GSGSSCDDIP TIDLIPQYLR FLQEWVENFC EQRQAKVKDV ITNCKSCKES GNKCKTECK TKCKDECEKY KKFIEACGTA GGGIGTAGSP WSKRWDQIYK RYSKHIEDAK RNRKAGTKNC GTSSTTNAAA STDENKCVQS DIDSFFKHL IDIGLTTPSS YLSNVLDDNI CGADKAPWTT YTTYTTTEKC NKERDKSKSQ SSDTLVVVNV PSPLGNTPYR Y KYACQCKI PTNEETCDDR KEYMNQWSCG SARTMKRGYK NDNYELCKYN GVDVKPTTVR SNSSKLDGND VTFFNLFEQW NK EIQYQIE QYMTNANISC IDEKEVLDSV SDEGTPKVRG GYEDGRNNNT DQGTNCKEKC KCYKLWIEKI NDQWGKQKDN YNK FRSKQI YDANKGSQNK KVVSLSNFLF FSCWEEYIQK YFNGDWSKIK NIGSDTFEFL IKKCGNNSAH GEEIFSEKLK NAEK KCKEN ESTDTNINKS ETSCDLNATN YIRGCQSKTY DGKIFPGKGG EKQWICKDTI IHGDTNGACI PPRTQNLCVG ELWDK SYGG RSNIKNDTKE LLKEKIKNAI HKETELLYEY HDTGTAIISK NDKKGQKGKN DPNGLPKGFC HAVQRSFIDY KNMILG TSV NIYEHIGKLQ EDIKKIIEKG TPQQKDKIGG VGSSTENVNA WWKGIEREMW DAVRCAITKI NKKNNNSIFN GDECGVS PP TGNDEDQSVS WFKEWGEQFC IERLRYEQNI REACTINGKN EKKCINSKSG QGDKIQGACK RKCEKYKKYI SEKKQEWD K QKTKYENKYV GKSASDLLKE NYPECISANF DFIFNDNIEY KTYYPYGDYS SICSCEQVKY YKYNNAEKKN NKSLCYEKD NDMTWSKKYI KKLENGRSLE GVYVPPRRQQ LCLYELFPII IKNEEGMEKA KEELLETLQI VAEREAYYLW KQYNPTGKGI DDANKKACC AIRGSFYDLE DIIKGNDLVH DEYTKYIDSK LNEIFGSSNT NDIDTKRART DWWENETITN GTDRKTIRQL V WDAMQSGV RYAVEEKNEN FPLCMGVEHI GIAKPQFIRW LEEWTNEFCE KYTKYFEDMK SKCDPPKRAD TCGDNSNIEC KK ACANYTN WLNPKRIEWN GMSNYYNKIY RKSNKESEDG KDYSMIMAPT VIDYLNKRCH GEINGNYICC SCKNIGAYNT TSG TVNKKL QKKETECEEE KGPLDLMNEV LNKMDKKYSA HKMKCTEVYL EHVEEQLNEI DNAIKDYKLY PLDRCFDDQT KMKV CDLIA DAIGCKDKTK LDELDEWNDM DLRGTYNKHK GVLIPPRRRQ LCFSRIVRGP ANLRSLNEFK EEILKGAQSE GKFLG NYYK EHKDKEKALE AMKNSFYDYE DIIKGTDMLT NIEFKDIKIK LDRLLEKETN NTKKAEDWWK TNKKSIWNAM LCGYKK SGN KIIDPSWCTI PTTETPPQFL RWIKEWGTNV CIQKQEHKEY VKSKCSNVTN LGAQASESNN CTSEIKKYQE WSRKRSI QW ETISKRYKKY KRMDILKDVK EPDANTYLRE HCSKCPCGFN DMEEMNNNED NEKEAFKQIK EQVKIPAELE DVIYRIKH H EYDKGNDYIC NKYKNIHDRM KKNNGNFVTD NFVKKSWEIS NGVLIPPRRK NLFLYIDPSK ICEYKKDPKL FKDFIYWSA FTEVERLKKA YGGARAKVVH AMKYSFTDIG SIIKGDDMME KNSSDKIGKI LGDTDGQNEK RKKWWDMNKY HIWESMLCGY REAEGDTET NENCRFPDIE SVPQFLRWFQ EWSENFCDRR QKLYDKLNSE CISAECTNGS VDNSKCTHAC VNYKNYILTK K TEYEIQTN KYDNEFKNKN SNDKDAPDYL KEKCNDNKCE CLNKHIDDKN KTWKNPYETL EDTFKSKCDC PKPLPSPIKP DD LPPQADE PF

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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

Concentration8.6 mg/mL
BufferpH: 7.5 / Details: 20mM Tris pH 7.5, 125mM KCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Added 1mM FF8 as additive just before freezing.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 8081 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 940807
CTF correctionSoftware - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 102676
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 1
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

4p1t

,

2y8d

)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7b52:
VAR2CSA full ectodomain

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