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- EMDB-33538: 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-33538
TitleCryo-EM structure of human IgM-Fc in complex with the J chain and the DBL domain of DBLMSP
Map data
Sample
  • Complex: Ternary complex of human IgM-Fc with the J chain and the DBL domain of DBLMSP
    • Complex: Putative erythrocyte membrane protein
      • Protein or peptide: Putative erythrocyte membrane protein
    • Complex: Immunoglobulin heavy constant mu
      • Protein or peptide: Immunoglobulin heavy constant mu
    • Complex: Immunoglobulin J chain
      • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsmalaria / immunoglobin / 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 / pre-B cell allelic exclusion / 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 / pre-B cell allelic exclusion / IgM immunoglobulin complex / glomerular filtration / CD22 mediated BCR regulation / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of respiratory burst / humoral immune response / Scavenging of heme from plasma / complement activation, classical pathway / antigen binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / antibacterial humoral response / protein-macromolecule adaptor activity / protein-containing complex assembly / defense response to Gram-negative bacterium / blood microparticle / adaptive immune response / Potential therapeutics for SARS / 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
Merozoite surface protein-type / Merozoite surface protein (SPAM) / Immunoglobulin J chain / Immunoglobulin J chain / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...Merozoite surface protein-type / Merozoite surface protein (SPAM) / Immunoglobulin J chain / Immunoglobulin J chain / 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
Putative erythrocyte membrane protein / Immunoglobulin J chain / Immunoglobulin heavy constant mu
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsShen H / Ji 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 3, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33538.png

Downloads & links

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Map

FileDownload / File: emd_33538.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.142
Minimum - Maximum-0.71727985 - 1.1100816
Average (Standard dev.)0.00085192936 (±0.02423944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33538_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_33538_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 with the J chain and the DBL doma...

EntireName: Ternary complex of human IgM-Fc with the J chain and the DBL domain of DBLMSP
Components
  • Complex: Ternary complex of human IgM-Fc with the J chain and the DBL domain of DBLMSP
    • Complex: Putative erythrocyte membrane protein
      • Protein or peptide: Putative erythrocyte membrane protein
    • Complex: Immunoglobulin heavy constant mu
      • Protein or peptide: Immunoglobulin heavy constant mu
    • Complex: Immunoglobulin J chain
      • 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 with the J chain and the DBL doma...

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

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Supramolecule #2: Putative erythrocyte membrane protein

SupramoleculeName: Putative erythrocyte membrane protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Immunoglobulin heavy constant mu

SupramoleculeName: Immunoglobulin heavy constant mu / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Immunoglobulin J chain

SupramoleculeName: Immunoglobulin J chain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: Putative erythrocyte membrane protein

MacromoleculeName: Putative erythrocyte membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 75.107406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DSNLRNGLLN NSLDLTNGLN NKDNSFIDSK IEEHENKSYQ NKDNNISIVG QDVPITSVDS SKIINANDLE GNSIDDTKGL SVTNSGFDD GSAFGGGLPF SGYSPLQGNH NKCPDENFCK GIKNVLSCPP KNSTGRNGDW ISVAVKESST TNKGVLVPPR R KKLCLRNI ...String:
DSNLRNGLLN NSLDLTNGLN NKDNSFIDSK IEEHENKSYQ NKDNNISIVG QDVPITSVDS SKIINANDLE GNSIDDTKGL SVTNSGFDD GSAFGGGLPF SGYSPLQGNH NKCPDENFCK GIKNVLSCPP KNSTGRNGDW ISVAVKESST TNKGVLVPPR R KKLCLRNI NQVWHRIKDE KNFKEEFVKV ALGESNALMK HYKEKNLNAL TAIKYGFSDM GDIIKGTDLI DYQITKNINR AL DKILGNE TSNDKIKKRV DWWEANKSAF WDAFMCGYKV HIGNKPCPEH DNMDRIPQYL RWFREWGTYV CSEYKNKFEN VIE LCNVRQ ITNQNDSQLL EISKEDKCKG ALKHYEEWVN RRRPEWKGQC DKFEKEKSKY EDTKSRTAEI YLKEICSECD CKYK DLDNT FKEFKDNVTL LKAVIDNKKN QDSLTTTSLS TSINSVRDSS NLDQRGNITT SQGNSHRATV VQQADQTNRL DNVNS VTQR GNNNYNNNLE RGLGSGALPG TNIITEEKYS LELIKLTSKD EEDIIKHNED VREEIEEQQE DIEEDEEELE NEGEET KEE DDEEKNETND TEDTDDTEDT EDIEEENEEK ELSNQQQSEK KSISKVDEDS YRILSVSYKD NNEVKNVAES IVKKLFS LF NDNNNLETIF KGLT

UniProtKB: Putative erythrocyte membrane protein

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Macromolecule #2: Immunoglobulin heavy constant mu

MacromoleculeName: Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 2 / 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 #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
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 #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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 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: PDB ENTRY
PDB model - PDB ID:

6kxs

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 391618
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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