+Open data
-Basic information
Entry | Database: PDB / ID: 7jg2 | |||||||||
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Title | Secretory Immunoglobin A (SIgA) | |||||||||
Components |
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Keywords | IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information Scavenging of heme from plasma / polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / 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 ...Scavenging of heme from plasma / polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / 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 / Cell surface interactions at the vascular wall / detection of chemical stimulus involved in sensory perception of bitter taste / glomerular filtration / phosphatidylcholine binding / peptidoglycan binding / epidermal growth factor receptor binding / receptor clustering / positive regulation of respiratory burst / immunoglobulin receptor binding / humoral immune response / regulation of immune response / Neutrophil degranulation / antigen binding / epidermal growth factor receptor signaling pathway / recycling endosome membrane / antibacterial humoral response / protein-macromolecule adaptor activity / single-stranded DNA binding / protein-containing complex assembly / adaptive immune response / receptor complex / innate immune response / endoplasmic reticulum / protein homodimerization activity / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Kumar Bharathkar, S. / Parker, B.P. / Malyutin, A.G. / Stadtmueller, B.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2020 Title: The structures of secretory and dimeric immunoglobulin A. Authors: Sonya Kumar Bharathkar / Benjamin W Parker / Andrey G Malyutin / Nandan Haloi / Kathryn E Huey-Tubman / Emad Tajkhorshid / Beth M Stadtmueller / Abstract: Secretory (S) Immunoglobulin (Ig) A is the predominant mucosal antibody, which binds pathogens and commensal microbes. SIgA is a polymeric antibody, typically containing two copies of IgA that ...Secretory (S) Immunoglobulin (Ig) A is the predominant mucosal antibody, which binds pathogens and commensal microbes. SIgA is a polymeric antibody, typically containing two copies of IgA that assemble with one joining-chain (JC) to form dimeric (d) IgA that is bound by the polymeric Ig-receptor ectodomain, called secretory component (SC). Here, we report the cryo-electron microscopy structures of murine SIgA and dIgA. Structures reveal two IgAs conjoined through four heavy-chain tailpieces and the JC that together form a β-sandwich-like fold. The two IgAs are bent and tilted with respect to each other, forming distinct concave and convex surfaces. In SIgA, SC is bound to one face, asymmetrically contacting both IgAs and JC. The bent and tilted arrangement of complex components limits the possible positions of both sets of antigen-binding fragments (Fabs) and preserves steric accessibility to receptor-binding sites, likely influencing antigen binding and effector functions. | |||||||||
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 | 7jg2.cif.gz | 516.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jg2.ent.gz | 440.3 KB | Display | PDB format |
PDBx/mmJSON format | 7jg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jg2_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7jg2_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7jg2_validation.xml.gz | 63.8 KB | Display | |
Data in CIF | 7jg2_validation.cif.gz | 92.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/7jg2 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/7jg2 | HTTPS FTP |
-Related structure data
Related structure data | 22310MC 7jg1C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 6 molecules ABCDEJ
#1: Protein | Mass: 37976.891 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Genes encoding the mus musculus IgA HC constant region and the lambda LC constant region were fused with HC and LC variable region sequences to create complete HC and LC sequences. The HC ...Details: Genes encoding the mus musculus IgA HC constant region and the lambda LC constant region were fused with HC and LC variable region sequences to create complete HC and LC sequences. The HC and LC variable region is not modeled in this structure. Since authors have chosen not to provide complete sample sequence of the HC and LC variable region the UNKs were not included in the sequence. Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igh / Production host: Homo sapiens (human) / References: UniProt: Q99M22, UniProt: P01878*PLUS #2: Protein | | Mass: 61257.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pigr / Plasmid: PLASMID / Details (production host): pD2610-v1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: O70570 #3: Protein | | Mass: 15637.499 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Jchain, Igj / Plasmid: pD2610-v1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P01592 |
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-Sugars , 4 types, 8 molecules
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | N |
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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: Secretory Immunoglobin A / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Pelco easiGlow - 20 mA current / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 292 K Details: Wait time - 0s Drain time - 0s Blot time - 6s Blot Force - 5 |
-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 / Nominal magnification: 130000 X / Calibrated magnification: 76687 X / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
Software | Name: PHENIX / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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Image processing | Details: Super resolution images were collected. During motion correction, movies were binned by 2. | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 956981 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 229252 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: THROUGHOUT | ||||||||||||||||||||||||
Displacement parameters | Biso max: 180.28 Å2 / Biso mean: 85.8474 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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