[English] 日本語
Yorodumi
- EMDB-34399: IgM-var2CSA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34399
TitleIgM-var2CSA complex
Map data
Sample
  • Complex: IgM-var2CSA complex
    • Complex: IgM, IgJ
    • Complex: var2CSA
      • Protein or peptide: Erythrocyte membrane protein 1
    • Protein or peptide: Immunoglobulin heavy constant mu
    • Protein or peptide: Immunoglobulin J chain
Keywordsvar2CSA / IgM / Placental malaria / P.falciparum / CELL ADHESION / CELL ADHESION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


hexameric IgM immunoglobulin complex / dimeric IgA immunoglobulin complex / IgM B cell receptor complex / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA binding / glomerular filtration / IgM immunoglobulin complex ...hexameric IgM immunoglobulin complex / dimeric IgA immunoglobulin complex / IgM B cell receptor complex / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA binding / glomerular filtration / IgM immunoglobulin complex / pre-B cell allelic exclusion / CD22 mediated BCR regulation / positive regulation of respiratory burst / humoral immune response / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Cell surface interactions at the vascular wall / antigen binding / B cell receptor signaling pathway / protein-macromolecule adaptor activity / antibacterial humoral response / protein-containing complex assembly / defense response to Gram-negative bacterium / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / innate immune response / cell surface / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin J chain / Immunoglobulin J chain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin J chain / Immunoglobulin heavy constant mu
Similarity search - Component
Biological speciesHomo sapiens (human) / Plasmodiupm falciparum (malaria parasite P. falciparum) / Plasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsAkhouri RR / Goel S / Skoglund U
Funding support Japan, 1 items
OrganizationGrant numberCountry
Other governmentcore grant Japan
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-electron microscopy of IgM-VAR2CSA complex reveals IgM inhibits binding of Plasmodium falciparum to Chondroitin Sulfate A.
Authors: Reetesh Raj Akhouri / Suchi Goel / Ulf Skoglund /
Abstract: Placental malaria is caused by Plasmodium falciparum-infected erythrocytes (IEs) adhering to chondroitin sulfate proteoglycans in placenta via VAR2CSA-type PfEMP1. Human pentameric immunoglobulin M ...Placental malaria is caused by Plasmodium falciparum-infected erythrocytes (IEs) adhering to chondroitin sulfate proteoglycans in placenta via VAR2CSA-type PfEMP1. Human pentameric immunoglobulin M (IgM) binds to several types of PfEMP1, including VAR2CSA via its Fc domain. Here, a 3.6 Å cryo-electron microscopy map of the IgM-VAR2CSA complex reveals that two molecules of VAR2CSA bind to the Cµ4 of IgM through their DBL3X and DBL5ε domains. The clockwise and anti-clockwise rotation of the two VAR2CSA molecules on opposite faces of IgM juxtaposes C-termini of both VAR2CSA near the J chain, where IgM creates a wall between both VAR2CSA molecules and hinders its interaction with its receptor. To support this, we show when VAR2CSA is bound to IgM, its staining on IEs as well as binding of IEs to chondroitin sulfate A in vitro is severely compromised.
History
DepositionSep 27, 2022-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34399.png

Downloads & links

-
Map

FileDownload / File: emd_34399.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.00805
Minimum - Maximum-0.018359132 - 0.04730232
Average (Standard dev.)-0.000045081913 (±0.0010604718)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 594.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_34399_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_34399_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34399_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : IgM-var2CSA complex

EntireName: IgM-var2CSA complex
Components
  • Complex: IgM-var2CSA complex
    • Complex: IgM, IgJ
    • Complex: var2CSA
      • Protein or peptide: Erythrocyte membrane protein 1
    • Protein or peptide: Immunoglobulin heavy constant mu
    • Protein or peptide: Immunoglobulin J chain

-
Supramolecule #1: IgM-var2CSA complex

SupramoleculeName: IgM-var2CSA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: IgM, IgJ

SupramoleculeName: IgM, IgJ / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: var2CSA

SupramoleculeName: var2CSA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Plasmodiupm falciparum (malaria parasite P. falciparum)

-
Macromolecule #1: Immunoglobulin heavy constant mu

MacromoleculeName: Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 1 / Details: IgM / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.48952 KDa
SequenceString: GSASAPTLFP LVSCENSPSD TSSVAVGCLA QDFLPDSITF SWKYKNNSDI SSTRGFPSVL RGGKYAATSQ VLLPSKDVMQ GTDEHVVCK VQHPNGNKEK NVPLPVIAEL PPKVSVFVPP RDGFFGNPRK SKLICQATGF SPRQIQVSWL REGKQVGSGV T TDQVQAEA ...String:
GSASAPTLFP LVSCENSPSD TSSVAVGCLA QDFLPDSITF SWKYKNNSDI SSTRGFPSVL RGGKYAATSQ VLLPSKDVMQ GTDEHVVCK VQHPNGNKEK NVPLPVIAEL PPKVSVFVPP RDGFFGNPRK SKLICQATGF SPRQIQVSWL REGKQVGSGV T TDQVQAEA KESGPTTYKV TSTLTIKESD WLGQSMFTCR VDHRGLTFQQ NASSMCVPDQ DTAIRVFAIP PSFASIFLTK ST KLTCLVT DLTTYDSVTI SWTRQNGEAV KTHTNISESH PNATFSAVGE ASICEDDWNS GERFTCTVTH TDLPSPLKQT ISR PKGVAL HRPDVYLLPP AREQLNLRES ATITCLVTGF SPADVFVQWM QRGQPLSPEK YVTSAPMPEP QAPGRYFAHS ILTV SEEEW NTGETYTCVV AHEALPNRVT ERTVDKSTGK PTLYNVSLVM SDTAGTCY

UniProtKB: Immunoglobulin heavy constant mu

-
Macromolecule #2: Erythrocyte membrane protein 1

MacromoleculeName: Erythrocyte membrane protein 1 / type: protein_or_peptide / ID: 2 / Details: plasmoDB-ID: PfIT_120006100 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 311.015688 KDa
Recombinant expressionOrganism: Drosophila (fruit flies)
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 PFLESRGPFE GKPIPNPLLG LDSTRTGHHH HHH

-
Macromolecule #3: Immunoglobulin J chain

MacromoleculeName: Immunoglobulin J chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.483329 KDa
SequenceString:
EDERIVLVDN KCKCARITSR IIRSSEDPNE DIVERNIRII VPLNNRENIS DPTSPLRTRF VYHLSDLCKK CDPTEVELDN QIVTATQSN ICDEDSATET CYTYDRNKCY TAVVPLVYGG ETKMVETALT PDACYPD

UniProtKB: Immunoglobulin J chain

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kxs

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 371049
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
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://pdbjlvh1.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