[English] 日本語
Yorodumi
- EMDB-16415: HB3VAR03 apo headstructure (PfEMP1 A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16415
TitleHB3VAR03 apo headstructure (PfEMP1 A)
Map data
Sample
  • Complex: Multidomain architecture of PfEMP1 A
    • Protein or peptide: PfEMP1Plasmodium falciparum erythrocyte membrane protein 1
KeywordsPlasmodium falciparum / Cerebral Malaria / PfEMP1 / EPCR / Cell adhesion
Function / homology
Function and homology information


host cell surface receptor binding / membrane
Similarity search - Function
: / 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 / PFEMP1 DBL domain / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum HB3 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 29, 2022-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16415.png

Downloads & links

-
Map

FileDownload / File: emd_16415.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.0932204 - 2.2085094
Average (Standard dev.)0.000094038056 (±0.05068671)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_16415_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16415_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Multidomain architecture of PfEMP1 A

EntireName: Multidomain architecture of PfEMP1 A
Components
  • Complex: Multidomain architecture of PfEMP1 A
    • Protein or peptide: PfEMP1Plasmodium falciparum erythrocyte membrane protein 1

-
Supramolecule #1: Multidomain architecture of PfEMP1 A

SupramoleculeName: Multidomain architecture of PfEMP1 A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum HB3 (eukaryote)
Molecular weightTheoretical: 145 KDa

-
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: 145.128734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 750035
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more