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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | HB3VAR03 apo headstructure (PfEMP1 A) | |||||||||
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![]() | Plasmodium falciparum / Cerebral Malaria / PfEMP1 / EPCR / Cell adhesion | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Raghavan SSR / Lavstsen T / Wang KT | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 52.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.8 KB 14.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 201.9 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 95.7 MB 95.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 784.7 KB | Display | ![]() |
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Full document | ![]() | 784.3 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c3yMC ![]() 8c44C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_16415_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16415_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Multidomain architecture of PfEMP1 A
Entire | Name: Multidomain architecture of PfEMP1 A |
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Components |
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-Supramolecule #1: Multidomain architecture of PfEMP1 A
Supramolecule | Name: Multidomain architecture of PfEMP1 A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 145 KDa |
-Macromolecule #1: PfEMP1
Macromolecule | Name: PfEMP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 145.128734 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 FCTNENNENG KNYEQWKCYY DNKKNNNKCK MEINIA NSK LKNKITSFDE FFDFWVRKLL IDTIKWETEL TYCINNTDVT DCNKCNKNCV 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 GSAHIVMVDA YKPTK UniProtKB: PfEMP1 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 |