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- EMDB-16416: HB3VAR03 apo headstructure (PfEMP1 A) complexed with EPCR -

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Basic information

Entry
Database: EMDB / ID: EMD-16416
TitleHB3VAR03 apo headstructure (PfEMP1 A) complexed with EPCR
Map data
Sample
  • Complex: Multidomain PFEMP1 A complexed with EPCR
    • Protein or peptide: PfEMP1
  • Protein or peptide: Endothelial protein C receptor
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsPlasmodium falciparum / Cerebral Malaria / PfEMP1 / EPCR / Cell adhesion
Function / homology
Function and homology information


negative regulation of coagulation / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / blood coagulation / signaling receptor activity / host cell surface receptor binding / focal adhesion / centrosome / perinuclear region of cytoplasm / cell surface ...negative regulation of coagulation / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / blood coagulation / signaling receptor activity / host cell surface receptor binding / focal adhesion / centrosome / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Endothelial protein C receptor / : / PfEMP1 protein, CIDRalpha1 domain / Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment / N-terminal segments of PfEMP1 / Cysteine-rich interdomain region 1 gamma / Cysteine-Rich Interdomain Region 1 gamma / Duffy-binding-like domain, C-terminal subdomain / Duffy-binding-like domain / PFEMP1 DBL domain ...Endothelial protein C receptor / : / PfEMP1 protein, CIDRalpha1 domain / Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment / N-terminal segments of PfEMP1 / Cysteine-rich interdomain region 1 gamma / Cysteine-Rich Interdomain Region 1 gamma / Duffy-binding-like domain, C-terminal subdomain / Duffy-binding-like domain / PFEMP1 DBL domain / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain / MHC-I family domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein
Similarity search - Domain/homology
PfEMP1 / Endothelial protein C receptor
Similarity search - Component
Biological speciesPlasmodium falciparum HB3 (eukaryote) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRaghavan SSR / Lavstsen T / Wang KT
Funding support Denmark, 2 items
OrganizationGrant numberCountry
Danish Council for Independent Research9039-00285A Denmark
LundbeckfondenR344-2020-934 Denmark
CitationJournal: Structure / Year: 2023
Title: Endothelial protein C receptor binding induces conformational changes to severe malaria-associated group A PfEMP1.
Authors: Sai Sundar Rajan Raghavan / Louise Turner / Rasmus W Jensen / Nicolai Tidemand Johansen / Daniel Skjold Jensen / Pontus Gourdon / Jinqiu Zhang / Yong Wang / Thor Grundtvig Theander / Kaituo ...Authors: Sai Sundar Rajan Raghavan / Louise Turner / Rasmus W Jensen / Nicolai Tidemand Johansen / Daniel Skjold Jensen / Pontus Gourdon / Jinqiu Zhang / Yong Wang / Thor Grundtvig Theander / Kaituo Wang / Thomas Lavstsen /
Abstract: Severe Plasmodium falciparum malaria infections are caused by microvascular sequestration of parasites binding to the human endothelial protein C receptor (EPCR) via the multi-domain P. falciparum ...Severe Plasmodium falciparum malaria infections are caused by microvascular sequestration of parasites binding to the human endothelial protein C receptor (EPCR) via the multi-domain P. falciparum erythrocyte membrane protein 1 (PfEMP1) adhesion ligands. Using cryogenic electron microscopy (Cryo-EM) and PfEMP1 sequence diversity analysis, we found that group A PfEMP1 CIDRα1 domains interact with the adjacent DBLα1 domain through central, conserved residues of the EPCR-binding site to adopt a compact conformation. Upon EPCR binding, the DBLα1 domain is displaced, and the EPCR-binding helix of CIDRα1 is turned, kinked, and twisted to reach a rearranged, stable EPCR-bound conformation. The unbound conformation and the required transition to the EPCR-bound conformation may represent a conformational masking mechanism of immune evasion for the PfEMP1 family.
History
DepositionDec 31, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16416.png

Downloads & links

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Map

FileDownload / File: emd_16416.map.gz / Format: CCP4 / Size: 282.6 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 420 pix.
= 349.44 Å		0.83 Å/pix.
x 420 pix.
= 349.44 Å		0.83 Å/pix.
x 420 pix.
= 349.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-3.727024 - 5.6941657
Average (Standard dev.)-0.00015084808 (±0.06068787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 349.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_16416_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16416_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16416_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Multidomain PFEMP1 A complexed with EPCR

EntireName: Multidomain PFEMP1 A complexed with EPCR
Components
  • Complex: Multidomain PFEMP1 A complexed with EPCR
    • Protein or peptide: PfEMP1
  • Protein or peptide: Endothelial protein C receptor
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Multidomain PFEMP1 A complexed with EPCR

SupramoleculeName: Multidomain PFEMP1 A complexed with EPCR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Plasmodium falciparum HB3 (eukaryote)
Molecular weightTheoretical: 175 KDa

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Macromolecule #1: PfEMP1

MacromoleculeName: PfEMP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum HB3 (eukaryote)
Molecular weightTheoretical: 145.158766 KDa
Recombinant expressionOrganism: Spodoptera frugiperda granulovirus
SequenceString: MASSASKFSK IVVGNETHKS ARNVLEGFAK DIKGKASIDA EKHAYSLKGN LKDAKFNHDF FKIKSDMPGN PCYLDFAFHS NTPGNQREY RHPCARSMNK NLFNLEGAVC TNSKIKGNEE KINGAGACAP YRRRHICDLN LEHIDVHNVQ NIHDLLGNVL V TAKYEGES ...String:
MASSASKFSK IVVGNETHKS ARNVLEGFAK DIKGKASIDA EKHAYSLKGN LKDAKFNHDF FKIKSDMPGN PCYLDFAFHS NTPGNQREY RHPCARSMNK NLFNLEGAVC TNSKIKGNEE KINGAGACAP YRRRHICDLN LEHIDVHNVQ NIHDLLGNVL V TAKYEGES IVEKHPNRGS SEVCTALARS FADIGDIIRG KDLYLGHEQG NNKLEARLKT IFQNIKNKNK SPLDKLSLEQ VR EYWWALN REDVWKALTC FADGSEEYFI QSSDKEHSFS SEYCGHEQGN VPTNLDYVPQ FLRWFDEWAD DFCRIKKIKL ENV KNACRD EKKRKYCSLN GFDCTQTIWK KGVLHRSNEC TGCLVKCNPY EIWLGNQREA FRKQKEKYEN EIKTYVHDTG ISNS NINNE YYKEFYKILK NNNYETANEF IKLLNEGRYC NKKEKIEEEE DIDFTNTNEK GTFYRSDYCQ VCPDCGVECK NETCT PKTV IYPDCGKNEK YEPPGDAKNT EINVINSGDK EGYIFEKLSE FCTNENTENI NNYEQWKCYY DNKKNNNKCK MEINIA NSK LKNKVTSFDE FFDFWVRKLL IDTIKWETEL TYCINNTDKF WCNKCNKNCV CFDKWVKQKE DEWTNIMKLF TNKHDIP KK YYLNINDLFD SFFFQVIYKF NEGEAKWNEL KENLKKQIAS SKANNGTKDS EAAIKVLFNH IKEIATICKD NNTNEGCD P SVDSKTNSCG KNTKAGSDKV ISVKQIAQYY KRIAHKQLNE RGSRSALKGD ASKGTYKKNG TPSNLKEICE ITAKHSNDS RRDGEPCTGK DGGQVRVRTK IGTPWTKIVE INKTSYKEVF LPPRRQHMCT SNLEHLNTGN KGLKDGKLAI HSLLGDVLLA AKEQANFIK NKYKRQKASN GFKDKGTICR AIRYSYADLG DIIKGTDLWE ANPGEKNTQR RLKTVFGIIK KNMPGIKDNQ K YKDDEKNN PPYKLLREDW WEANRDQVWQ AMKCAMKNGI TCGSSDHTPL DDYIPQKLRW LTEWAEWYCK AQSKEYEKLK EK CKECKGN DQCTQDTPDC EKCKAACKKY GKNIKTWEDQ WKVISSKYKE LYKQAEIYAG NGGPGYYNTK VQEEDKPVVD FLY NLYLQN GGKKGPPPDT HPSKSVTAPL KQVATVDTPS TVYSTPEGYI HQEAAMDCKQ QHVFCDDNSG GKDDNKQYAF RHQP HDYDE ALRCDQRDKP PPESKKVEKA KKEKDENDDG GSHHHHHHGG GSAHIVVDAY KPTK

UniProtKB: PfEMP1

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Macromolecule #2: Endothelial protein C receptor

MacromoleculeName: Endothelial protein C receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.471928 KDa
Recombinant expressionOrganism: Spodoptera frugiperda granulovirus
SequenceString:
QRLHMLQISY FRDPYHVWYQ GNASLGGHLT HVLEGPDTNT TIIQLQPLQE PESWARTQSG LQSYLLQFHG LVRLVHQERT LAFPLTIRC FLGCELPPEG SRAHVFFEVA VNGSSFVSFR PERALWQADT QVTSGVVTFT LQQLNAYNRT RYELREFLED T CVQYVQKH

UniProtKB: Endothelial protein C receptor

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Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.7 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 505000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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