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Yorodumi- PDB-7jic: Structure of human CD19-CD81 co-receptor complex bound to coltuxi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jic | ||||||||||||
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Title | Structure of human CD19-CD81 co-receptor complex bound to coltuximab Fab fragment | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / tetraspanin / Fab / complex | ||||||||||||
Function / homology | Function and homology information regulation of B cell activation / positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / antigen receptor-mediated signaling pathway / CD4-positive, alpha-beta T cell costimulation / osteoclast fusion / B-1 B cell differentiation / positive regulation of B cell receptor signaling pathway / myoblast fusion involved in skeletal muscle regeneration / positive regulation of inflammatory response to antigenic stimulus ...regulation of B cell activation / positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / antigen receptor-mediated signaling pathway / CD4-positive, alpha-beta T cell costimulation / osteoclast fusion / B-1 B cell differentiation / positive regulation of B cell receptor signaling pathway / myoblast fusion involved in skeletal muscle regeneration / positive regulation of inflammatory response to antigenic stimulus / regulation of B cell receptor signaling pathway / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of macrophage migration / macrophage fusion / immunological synapse formation / tetraspanin-enriched microdomain / transferrin receptor binding / positive regulation of T-helper 2 cell cytokine production / protein localization to lysosome / B cell proliferation involved in immune response / positive regulation of protein exit from endoplasmic reticulum / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell proliferation / humoral immune response mediated by circulating immunoglobulin / cholesterol binding / positive regulation of T cell receptor signaling pathway / cellular response to low-density lipoprotein particle stimulus / immunoglobulin mediated immune response / immunological synapse / positive regulation of B cell proliferation / positive regulation of receptor clustering / basal plasma membrane / positive regulation of release of sequestered calcium ion into cytosol / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / protein localization to plasma membrane / B cell receptor signaling pathway / regulation of protein stability / receptor internalization / Constitutive Signaling by Aberrant PI3K in Cancer / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / virus receptor activity / PIP3 activates AKT signaling / MHC class II protein complex binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / basolateral plasma membrane / vesicle / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / external side of plasma membrane / focal adhesion / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Susa, K.J. / Rawson, S. / Kruse, A.C. / Blacklow, S.C. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Science / Year: 2021 Title: Cryo-EM structure of the B cell co-receptor CD19 bound to the tetraspanin CD81. Authors: Katherine J Susa / Shaun Rawson / Andrew C Kruse / Stephen C Blacklow / Abstract: Signaling through the CD19-CD81 co-receptor complex, in combination with the B cell receptor, is a critical determinant of B cell development and activation. It is unknown how CD81 engages CD19 to ...Signaling through the CD19-CD81 co-receptor complex, in combination with the B cell receptor, is a critical determinant of B cell development and activation. It is unknown how CD81 engages CD19 to enable co-receptor function. Here, we report a 3.8-angstrom structure of the CD19-CD81 complex bound to a therapeutic antigen-binding fragment, determined by cryo-electron microscopy (cryo-EM). The structure includes both the extracellular domains and the transmembrane helices of the complex, revealing a contact interface between the ectodomains that drives complex formation. Upon binding to CD19, CD81 opens its ectodomain to expose a hydrophobic CD19-binding surface and reorganizes its transmembrane helices to occlude a cholesterol binding pocket present in the apoprotein. Our data reveal the structural basis for CD19-CD81 complex assembly, providing a foundation for rational design of therapies for B cell dysfunction. | ||||||||||||
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 | 7jic.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jic.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 7jic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/7jic ftp://data.pdbj.org/pub/pdb/validation_reports/ji/7jic | HTTPS FTP |
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-Related structure data
Related structure data | 22344MC 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: Protein | Mass: 36031.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD19 / Plasmid: pcDNA3.1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P15391 |
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#2: Protein | Mass: 26444.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD81, TAPA1, TSPAN28 / Plasmid: pcDNA3.1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P60033 |
#3: Antibody | Mass: 24828.639 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pFUSE / Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
#4: Antibody | Mass: 23211.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pd2610-v5 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 0.110 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K Details: Blot for 4.5-5.5 seconds with a blot force of 15-16. |
-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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 6 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2798945 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 244583 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 114.72 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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