+Open data
-Basic information
Entry | Database: PDB / ID: 6lx3 | ||||||
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Title | Cryo-EM structure of human secretory immunoglobulin A | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin / dimer / transcytosis / secreted | ||||||
Function / homology | Function and homology information polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / kappa-type opioid receptor binding / dimeric IgA immunoglobulin complex / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / polymeric immunoglobulin binding / interleukin-2 receptor binding / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex ...polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / kappa-type opioid receptor binding / dimeric IgA immunoglobulin complex / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / polymeric immunoglobulin binding / interleukin-2 receptor binding / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / positive regulation of plasma cell differentiation / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / Fc receptor signaling pathway / IgA binding / positive regulation of tissue remodeling / glomerular filtration / negative regulation of T-helper 17 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / detection of chemical stimulus involved in sensory perception of bitter taste / IgA immunoglobulin complex / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / activated T cell proliferation / natural killer cell activation / positive regulation of regulatory T cell differentiation / : / kinase activator activity / negative regulation of B cell apoptotic process / IgG immunoglobulin complex / Interleukin-2 signaling / positive regulation of immunoglobulin production / azurophil granule membrane / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / receptor clustering / positive regulation of respiratory burst / humoral immune response / T cell differentiation / Interleukin receptor SHC signaling / Scavenging of heme from plasma / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / immunoglobulin complex, circulating / immunoglobulin receptor binding / negative regulation of protein phosphorylation / cytokine activity / complement activation, classical pathway / Cell surface interactions at the vascular wall / antigen binding / B cell receptor signaling pathway / growth factor activity / epidermal growth factor receptor signaling pathway / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of type II interferon production / cell-cell signaling / protein-macromolecule adaptor activity / positive regulation of cytosolic calcium ion concentration / antibacterial humoral response / RAF/MAP kinase cascade / positive regulation of cell growth / carbohydrate binding / protein-containing complex assembly / response to ethanol / adaptive immune response / transcription by RNA polymerase II / receptor complex / blood microparticle / cell adhesion / immune response / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å | ||||||
Authors | Wang, Y. / Wang, G. / Li, Y. / Xiao, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Res / Year: 2020 Title: Structural insights into secretory immunoglobulin A and its interaction with a pneumococcal adhesin. Authors: Yuxin Wang / Guopeng Wang / Yaxin Li / Qinyu Zhu / Hao Shen / Ning Gao / Junyu Xiao / Abstract: Secretory Immunoglobulin A (SIgA) is the most abundant antibody at the mucosal surface. It possesses two additional subunits besides IgA: the joining chain (J-chain) and secretory component (SC). SC ...Secretory Immunoglobulin A (SIgA) is the most abundant antibody at the mucosal surface. It possesses two additional subunits besides IgA: the joining chain (J-chain) and secretory component (SC). SC is the ectodomain of the polymeric immunoglobulin receptor (pIgR), which functions to transport IgA to the mucosa. How the J-chain and pIgR/SC facilitate the assembly and secretion of SIgA remains incompletely understood. Furthermore, during the infection of Streptococcus pneumoniae, the pneumococcal adhesin SpsA hijacks pIgR/SC and SIgA to gain entry to human cells and evade host defense. How SpsA targets pIgR/SC and SIgA also remains elusive. Here we report a cryo-electron microscopy structure of the Fc region of IgA1 (Fcα) in complex with the J-chain and SC (Fcα-J-SC), which reveals the organization principle of SIgA. We also present a structure of Fcα-J-SC complexed with SpsA, which uncovers the specific interactions between SpsA and human pIgR/SC. These results advance the molecular understanding of SIgA and shed light on S. pneumoniae pathogenesis. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6lx3.cif.gz | 265.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lx3.ent.gz | 215.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lx3_validation.pdf.gz | 1018.8 KB | Display | wwPDB validaton report |
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Full document | 6lx3_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6lx3_validation.xml.gz | 54.5 KB | Display | |
Data in CIF | 6lx3_validation.cif.gz | 83.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/6lx3 ftp://data.pdbj.org/pub/pdb/validation_reports/lx/6lx3 | HTTPS FTP |
-Related structure data
Related structure data | 30004MC 6lxwC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Antibody | Mass: 31445.693 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL2, IGHA1 / Production host: Homo sapiens (human) / References: UniProt: P60568, UniProt: P01876 #2: Protein | | Mass: 19225.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JCHAIN, IGCJ, IGJ / Production host: Homo sapiens (human) / References: UniProt: P01591 #3: Protein | | Mass: 63306.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIGR / Production host: Homo sapiens (human) / References: UniProt: P01833 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ternary complex of IgA-Fc with the J chain and pIgR/SC Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company | |||||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | |||||||||||||||
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM | |||||||||||||||
Electron lens | Mode: BRIGHT FIELD | |||||||||||||||
Image recording |
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-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 665589 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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