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- EMDB-33542: Cryo-EM structure of human IgM-Fc in complex with the J chain and... -

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Basic information

Entry
Database: EMDB / ID: EMD-33542
TitleCryo-EM structure of human IgM-Fc in complex with the J chain and the P. falciparum VAR2CSA FCR3
Map data
Sample
  • Complex: Ternary complex of human IgM-Fc in complex with the J chain and the P. falciparum VAR2CSA FCR3
    • Complex: P. falciparum VAR2CSA FCR3
      • Protein or peptide: Erythrocyte membrane protein 1
    • Complex: human IgM-Fc
      • Protein or peptide: Immunoglobulin heavy constant mu
      • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplex / antibody / IMMUNE SYSTEM
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 / host cell surface receptor binding / immune response / innate immune response / cell surface / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Plasmodium falciparum erythrocyte membrane protein 1, N-terminal / N-terminal segments of P. falciparum erythrocyte membrane protein / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment superfamily / Immunoglobulin J chain / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment / Immunoglobulin J chain / acidic terminal segments, variant surface antigen of PfEMP1 / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain ...Plasmodium falciparum erythrocyte membrane protein 1, N-terminal / N-terminal segments of P. falciparum erythrocyte membrane protein / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment superfamily / Immunoglobulin J chain / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment / Immunoglobulin J chain / acidic terminal segments, variant surface antigen of PfEMP1 / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain / 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 / Erythrocyte membrane protein 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsJi C / Xiao J
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2023
Title: Plasmodium falciparum has evolved multiple mechanisms to hijack human immunoglobulin M.
Authors: Chenggong Ji / Hao Shen / Chen Su / Yaxin Li / Shihua Chen / Thomas H Sharp / Junyu Xiao /
Abstract: Plasmodium falciparum causes the most severe malaria in humans. Immunoglobulin M (IgM) serves as the first line of humoral defense against infection and potently activates the complement pathway to ...Plasmodium falciparum causes the most severe malaria in humans. Immunoglobulin M (IgM) serves as the first line of humoral defense against infection and potently activates the complement pathway to facilitate P. falciparum clearance. A number of P. falciparum proteins bind IgM, leading to immune evasion and severe disease. However, the underlying molecular mechanisms remain unknown. Here, using high-resolution cryo-electron microscopy, we delineate how P. falciparum proteins VAR2CSA, TM284VAR1, DBLMSP, and DBLMSP2 target IgM. Each protein binds IgM in a different manner, and together they present a variety of Duffy-binding-like domain-IgM interaction modes. We further show that these proteins interfere directly with IgM-mediated complement activation in vitro, with VAR2CSA exhibiting the most potent inhibitory effect. These results underscore the importance of IgM for human adaptation of P. falciparum and provide critical insights into its immune evasion mechanism.
History
DepositionJun 5, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33542.png

Downloads & links

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Map

FileDownload / File: emd_33542.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.117457 - 1.6488439
Average (Standard dev.)0.001750503 (±0.027854007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33542_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33542_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of human IgM-Fc in complex with the J chain and t...

EntireName: Ternary complex of human IgM-Fc in complex with the J chain and the P. falciparum VAR2CSA FCR3
Components
  • Complex: Ternary complex of human IgM-Fc in complex with the J chain and the P. falciparum VAR2CSA FCR3
    • Complex: P. falciparum VAR2CSA FCR3
      • Protein or peptide: Erythrocyte membrane protein 1
    • Complex: human IgM-Fc
      • Protein or peptide: Immunoglobulin heavy constant mu
      • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ternary complex of human IgM-Fc in complex with the J chain and t...

SupramoleculeName: Ternary complex of human IgM-Fc in complex with the J chain and the P. falciparum VAR2CSA FCR3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #1-#2
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

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Supramolecule #2: P. falciparum VAR2CSA FCR3

SupramoleculeName: P. falciparum VAR2CSA FCR3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: human IgM-Fc

SupramoleculeName: human IgM-Fc / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2

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Macromolecule #1: Immunoglobulin heavy constant mu

MacromoleculeName: Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.875766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ASAWSHPQFE KGGGSGGGSG GSAWSHPQFE KIDTTIAELP PKVSVFVPPR DGFFGNPRKS KLICQATGFS PRQIQVSWLR EGKQVGSGV TTDQVQAEAK ESGPTTYKVT STLTIKESDW LGQSMFTCRV DHRGLTFQQN ASSMCVPDQD TAIRVFAIPP S FASIFLTK ...String:
ASAWSHPQFE KGGGSGGGSG GSAWSHPQFE KIDTTIAELP PKVSVFVPPR DGFFGNPRKS KLICQATGFS PRQIQVSWLR EGKQVGSGV TTDQVQAEAK ESGPTTYKVT STLTIKESDW LGQSMFTCRV DHRGLTFQQN ASSMCVPDQD TAIRVFAIPP S FASIFLTK STKLTCLVTD LTTYDSVTIS WTRQNGEAVK THTNISESHP NATFSAVGEA SICEDDWNSG ERFTCTVTHT DL PSPLKQT ISRPKGVALH RPDVYLLPPA REQLNLRESA TITCLVTGFS PADVFVQWMQ RGQPLSPEKY VTSAPMPEPQ APG RYFAHS ILTVSEEEWN TGETYTCVVA HEALPNRVTE RTVDKSTGKP TLYNVSLVMS DTAGTCY

UniProtKB: Immunoglobulin heavy constant mu

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Macromolecule #2: Immunoglobulin J chain

MacromoleculeName: Immunoglobulin J chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.483329 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EDERIVLVDN KCKCARITSR IIRSSEDPNE DIVERNIRII VPLNNRENIS DPTSPLRTRF VYHLSDLCKK CDPTEVELDN QIVTATQSN ICDEDSATET CYTYDRNKCY TAVVPLVYGG ETKMVETALT PDACYPD

UniProtKB: Immunoglobulin J chain

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Macromolecule #3: Erythrocyte membrane protein 1

MacromoleculeName: Erythrocyte membrane protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 306.371406 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 GEEIFNEKLK 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 LNEIFGSSDT NDIDTKRART DWWENETITN GTDRKTIRQL V WDAMQSGV RYAVEEKNEN FPLCMGVEHI GIAKPQFIRW LEEWTNEFCE KYTKYFEDMK SKCDPPKRAD TCGDNSNIEC KK ACANYTN WLNPKRIEWN GMSNYYNKIY RKSNKESEGG 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 RW 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 HHHHHHHH

UniProtKB: Erythrocyte membrane protein 1

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 10 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 690345
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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