+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20749 | |||||||||
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Title | Structure of dimeric sIgA complex | |||||||||
Map data | Main map of sIgA Dimer. | |||||||||
Sample |
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Keywords | immunoglobulin / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / Fc receptor signaling pathway / polymeric immunoglobulin binding / dimeric IgA immunoglobulin complex / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA binding ...polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / Fc receptor signaling pathway / polymeric immunoglobulin binding / dimeric IgA immunoglobulin complex / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA binding / detection of chemical stimulus involved in sensory perception of bitter taste / IgA immunoglobulin complex / glomerular filtration / IgG immunoglobulin complex / azurophil granule membrane / receptor clustering / positive regulation of respiratory burst / immunoglobulin complex, circulating / immunoglobulin receptor binding / humoral immune response / Scavenging of heme from plasma / complement activation, classical pathway / antigen binding / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / epidermal growth factor receptor signaling pathway / antibacterial humoral response / protein-macromolecule adaptor activity / protein-containing complex assembly / adaptive immune response / blood microparticle / receptor complex / immune response / innate immune response / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Kumar N / Arthur CP | |||||||||
Citation | Journal: Science / Year: 2020 Title: Structure of the secretory immunoglobulin A core. Authors: Nikit Kumar / Christopher P Arthur / Claudio Ciferri / Marissa L Matsumoto / Abstract: Secretory immunoglobulin A (sIgA) represents the immune system's first line of defense against mucosal pathogens. IgAs are transported across the epithelium, as dimers and higher-order polymers, by ...Secretory immunoglobulin A (sIgA) represents the immune system's first line of defense against mucosal pathogens. IgAs are transported across the epithelium, as dimers and higher-order polymers, by the polymeric immunoglobulin receptor (pIgR). Upon reaching the luminal side, sIgAs mediate host protection and pathogen neutralization. In recent years, an increasing amount of attention has been given to IgA as a novel therapeutic antibody. However, despite extensive studies, sIgA structures have remained elusive. Here, we determine the atomic resolution structures of dimeric, tetrameric, and pentameric IgA-Fc linked by the joining chain (JC) and in complex with the secretory component of the pIgR. We suggest a mechanism in which the JC templates IgA oligomerization and imparts asymmetry for pIgR binding and transcytosis. This framework will inform the design of future IgA-based therapeutics. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20749.map.gz | 200.5 MB | EMDB map data format | |
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Header (meta data) | emd-20749-v30.xml emd-20749.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
Images | emd_20749.png | 87.5 KB | ||
Filedesc metadata | emd-20749.cif.gz | 6.1 KB | ||
Others | emd_20749_additional.map.gz | 199.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20749 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20749 | HTTPS FTP |
-Validation report
Summary document | emd_20749_validation.pdf.gz | 517.4 KB | Display | EMDB validaton report |
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Full document | emd_20749_full_validation.pdf.gz | 517 KB | Display | |
Data in XML | emd_20749_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | emd_20749_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20749 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20749 | HTTPS FTP |
-Related structure data
Related structure data | 6ue7MC 6ue8C 6ue9C 6ueaC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20749.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Main map of sIgA Dimer. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0188 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: -150 sharpened map of sIgA Dimer complex.
File | emd_20749_additional.map | ||||||||||||
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Annotation | -150 sharpened map of sIgA Dimer complex. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : dimeric sIgA complex
Entire | Name: dimeric sIgA complex |
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Components |
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-Supramolecule #1: dimeric sIgA complex
Supramolecule | Name: dimeric sIgA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 188 KDa |
-Macromolecule #1: Immunoglobulin heavy constant alpha 1
Macromolecule | Name: Immunoglobulin heavy constant alpha 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 26.667172 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DYKDDDDKLV PRGSCHPRLS LHRPALEDLL LGSEANLTCT LTGLRDASGV TFTWTPSSGK SAVQGPPERD LCGCYSVSSV LPGCAEPWN HGKTFTCTAA YPESKTPLTA TLSKSGNTFR PEVHLLPPPS EELALNELVT LTCLARGFSP KDVLVRWLQG S QELPREKY ...String: DYKDDDDKLV PRGSCHPRLS LHRPALEDLL LGSEANLTCT LTGLRDASGV TFTWTPSSGK SAVQGPPERD LCGCYSVSSV LPGCAEPWN HGKTFTCTAA YPESKTPLTA TLSKSGNTFR PEVHLLPPPS EELALNELVT LTCLARGFSP KDVLVRWLQG S QELPREKY LTWASRQEPS QGTTTFAVTS ILRVAAEDWK KGDTFSCMVG HEALPLAFTQ KTIDRLAGKP THVNVSVVMA EV DGTCY UniProtKB: Immunoglobulin heavy constant alpha 1 |
-Macromolecule #2: Polymeric immunoglobulin receptor
Macromolecule | Name: Polymeric immunoglobulin receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 65.154094 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: KSPIFGPEEV NSVEGNSVSI TCYYPPTSVN RHTRKYWCRQ GARGGCITLI SSEGYVSSKY AGRANLTNFP ENGTFVVNIA QLSQDDSGR YKCGLGINSR GLSFDVSLEV SQGPGLLNDT KVYTVDLGRT VTINCPFKTE NAQKRKSLYK QIGLYPVLVI D SSGYVNPN ...String: KSPIFGPEEV NSVEGNSVSI TCYYPPTSVN RHTRKYWCRQ GARGGCITLI SSEGYVSSKY AGRANLTNFP ENGTFVVNIA QLSQDDSGR YKCGLGINSR GLSFDVSLEV SQGPGLLNDT KVYTVDLGRT VTINCPFKTE NAQKRKSLYK QIGLYPVLVI D SSGYVNPN YTGRIRLDIQ GTGQLLFSVV INQLRLSDAG QYLCQAGDDS NSNKKNADLQ VLKPEPELVY EDLRGSVTFH CA LGPEVAN VAKFLCRQSS GENCDVVVNT LGKRAPAFEG RILLNPQDKD GSFSVVITGL RKEDAGRYLC GAHSDGQLQE GSP IQAWQL FVNEESTIPR SPTVVKGVAG GSVAVLCPYN RKESKSIKYW CLWEGAQNGR CPLLVDSEGW VKAQYEGRLS LLEE PGNGT FTVILNQLTS RDAGFYWCLT NGDTLWRTTV EIKIIEGEPN LKVPGNVTAV LGETLKVPCH FPCKFSSYEK YWCKW NNTG CQALPSQDEG PSKAFVNCDE NSRLVSLTLN LVTRADEGWY WCGVKQGHFY GETAAVYVAV EERKAAGSRD VSLAKA DAA PDEKVLDSGF REIENKAIQD PRHHHHHH UniProtKB: Polymeric immunoglobulin receptor |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 15.611458 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: QEDERIVLVD NKCKCARITS RIIRSSEDPN EDIVERNIRI IVPLNNRENI SDPTSPLRTR FVYHLSDLCK KCDPTEVELD NQIVTATQS NICDEDSATE TCYTYDRNKC YTAVVPLVYG GETKMVETAL TPDACYPD UniProtKB: Immunoglobulin J chain |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 7 / 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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.18 mg/mL |
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Buffer | pH: 7.2 |
Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 5 sec. / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 10.0 sec. / Average electron dose: 51.91 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 233402 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: OTHER / Software - Name: cisTEM |