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- EMDB-33805: Cryo-EM structure of human IgM-Fc in complex with the J chain and... -
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Open data
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Basic information
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Title | Cryo-EM structure of human IgM-Fc in complex with the J chain and the DBL domain of DBLMSP2 | |||||||||
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![]() | malaria / immunoglobin / IMMUNE SYSTEM | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.32 Å | |||||||||
![]() | Shen H / Ji C / Xiao J | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 118.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.6 KB 17.6 KB | Display Display | ![]() |
Images | ![]() | 52.1 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 978.6 KB | Display | ![]() |
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Full document | ![]() | 978.1 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yg2MC ![]() 7y09C ![]() 7y0hC ![]() 7y0jC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33805_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33805_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Ternary complex of human IgM-Fc with the J chain and the DBL doma...
Entire | Name: Ternary complex of human IgM-Fc with the J chain and the DBL domain of DBLMSP2 |
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Components |
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-Supramolecule #1: Ternary complex of human IgM-Fc with the J chain and the DBL doma...
Supramolecule | Name: Ternary complex of human IgM-Fc with the J chain and the DBL domain of DBLMSP2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: Putative erythrocyte membrane protein
Supramolecule | Name: Putative erythrocyte membrane protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: Immunoglobulin heavy constant mu
Supramolecule | Name: Immunoglobulin heavy constant mu / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
-Supramolecule #4: Immunoglobulin J chain
Supramolecule | Name: Immunoglobulin J chain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 |
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-Macromolecule #1: DBLMSP2
Macromolecule | Name: DBLMSP2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 36.305992 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: TINLGFNKCP TEEICKDFSN LPQCRKNVHE RNNWLGSSVK NFSSDNKGVL VPPRRQSLCL RITLQDFRTK KKKEGDFEKF IYSYASSEA RKLRTIHNNN LEKAHQAIRY SFADIGNIIR GDDMMDTPTS KETITYLEKV LKIYNENNDK PKDAKKWWTE N RHHVWEAM ...String: TINLGFNKCP TEEICKDFSN LPQCRKNVHE RNNWLGSSVK NFSSDNKGVL VPPRRQSLCL RITLQDFRTK KKKEGDFEKF IYSYASSEA RKLRTIHNNN LEKAHQAIRY SFADIGNIIR GDDMMDTPTS KETITYLEKV LKIYNENNDK PKDAKKWWTE N RHHVWEAM MCGYQSAQKD NQCTGYGNID DIPQFLRWFR EWGTYVCEES EKNMNTLKAV CFPKQPRTEA NPALTVHENE MC SSTLKKY EEWYNKRKTE WTEQSIKYNN DKINYTDIKT LSPSEYLIEK CPECKCTKKN LQDVFELTFD UniProtKB: DBLMSP2 |
-Macromolecule #2: Immunoglobulin heavy constant mu
Macromolecule | Name: Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 41.875766 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #3: Immunoglobulin J chain
Macromolecule | Name: Immunoglobulin J chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 15.483329 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: EDERIVLVDN KCKCARITSR IIRSSEDPNE DIVERNIRII VPLNNRENIS DPTSPLRTRF VYHLSDLCKK CDPTEVELDN QIVTATQSN ICDEDSATET CYTYDRNKCY TAVVPLVYGG ETKMVETALT PDACYPD UniProtKB: Immunoglobulin J chain |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 10 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.1 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 458396 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |