[English] 日本語
Yorodumi
- EMDB-72651: HB3VAR03 CIDRa1.4 in complex with B57 and C50 fabs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72651
TitleHB3VAR03 CIDRa1.4 in complex with B57 and C50 fabs
Map data
Sample
  • Cell: Structure of HB3VAR03 CIDRa1.4 PfEMP1 protein in complex with B57 and C50 Fabs
    • Protein or peptide: B57 heavy chain
    • Protein or peptide: B57 light chain
    • Protein or peptide: C50 heavy chain
    • Protein or peptide: C50 light chain
    • Protein or peptide: PfEMP1
KeywordsMalaria / PfEMP1 / Cerebral malaria / broadly neutralizing antibodies / IMMUNE SYSTEM
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, C-terminal subdomain / Duffy-binding-like domain / PFEMP1 DBL domain ...: / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Plasmodium falciparum HB3 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsRaghavan SSR / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: To Be Published
Title: Structure of variant specific human monoclonal antibody B57 in complex with HB3VAR03 CIDRa1.4 PfEMP1 protein
Authors: Raghavan SSR / Ward AB
History
DepositionSep 9, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72651.png

Downloads & links

-
Map

FileDownload / File: emd_72651.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 261. Å		0.73 Å/pix.
x 360 pix.
= 261. Å		0.73 Å/pix.
x 360 pix.
= 261. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.7592934 - 1.0183554
Average (Standard dev.)0.0001295233 (±0.017230656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 261.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_72651_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_72651_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Structure of HB3VAR03 CIDRa1.4 PfEMP1 protein in complex with B57...

EntireName: Structure of HB3VAR03 CIDRa1.4 PfEMP1 protein in complex with B57 and C50 Fabs
Components
  • Cell: Structure of HB3VAR03 CIDRa1.4 PfEMP1 protein in complex with B57 and C50 Fabs
    • Protein or peptide: B57 heavy chain
    • Protein or peptide: B57 light chain
    • Protein or peptide: C50 heavy chain
    • Protein or peptide: C50 light chain
    • Protein or peptide: PfEMP1

-
Supramolecule #1: Structure of HB3VAR03 CIDRa1.4 PfEMP1 protein in complex with B57...

SupramoleculeName: Structure of HB3VAR03 CIDRa1.4 PfEMP1 protein in complex with B57 and C50 Fabs
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: B57 heavy chain

MacromoleculeName: B57 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.258014 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLVQSGAE VRKPGSSVKV SCKVSGGTFS IFGINWIRKA PGQGFEWMGG IVPQLGGPNY VKKFQGRVSF TADELTTTAY MELRSLTPE DSALYFCAKG AQTYALLYYF DSWGQGTLVT VSS

-
Macromolecule #2: B57 light chain

MacromoleculeName: B57 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.413427 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QSALTQPPSA SGSPGQSVTI SCTGTSSDIG GYNYVSWYQQ HPGKAPKVVI YDVTKRPSGV PDRFSGSKSG NTASLTVSGL QADDEAIYY CSSYAYNNNL VFGGGTSLAV L

-
Macromolecule #3: C50 heavy chain

MacromoleculeName: C50 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.40892 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLVESGGG VVQPGRSLRL SCAASGFTFE TYVMHWVRQT PGKGLEWVAL TSYDGKRKYY ADSVKGRFSA SRDNSENTVS LQMSSLSTE DTAVYYCVRS RHGYSFTNMD VWGRGTTVIV SS

-
Macromolecule #4: C50 light chain

MacromoleculeName: C50 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.818963 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
VSAAPGQTVT ISCSEYISNI GDNYVSWYQH VPGTAPRVVM SHYNERPSGI PDRFSGSKSG ASATLGITGL QTGDEADYYC GAWDDRLKI FVFGTATKVT VL

-
Macromolecule #5: PfEMP1

MacromoleculeName: PfEMP1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum HB3 (eukaryote)
Molecular weightTheoretical: 145.100688 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSSASKFSK IVVGNETHKS ARNVLEGFAK DIKGKASIDA EKHAYSLKGN LKDAKFNHDF FKIKSDMPGN PCYLDFAFHS NTPGNQREY RHPCARSMNK NLFNLEGAVC TNSKIKGNEE KINGAGACAP YRRRHICDLN LEHIDVHNVQ NIHDLLGNVL V TAKYEGES ...String:
MGSSASKFSK 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 LKNKVTSFDE 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 264864
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
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