+Open data
-Basic information
Entry | Database: PDB / ID: 6uja | ||||||||||||||||||||||||
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Title | Integrin alpha-v beta-8 in complex with pro-TGF-beta1 | ||||||||||||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / glycoprotein / adhesion / signaling | ||||||||||||||||||||||||
Function / homology | Function and homology information Platelet degranulation / Cell surface interactions at the vascular wall / Molecules associated with elastic fibres / TGF-beta receptor signaling activates SMADs / Syndecan interactions / RUNX3 regulates CDKN1A transcription / RUNX3 regulates p14-ARF / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of RUNX3 expression and activity ...Platelet degranulation / Cell surface interactions at the vascular wall / Molecules associated with elastic fibres / TGF-beta receptor signaling activates SMADs / Syndecan interactions / RUNX3 regulates CDKN1A transcription / RUNX3 regulates p14-ARF / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of RUNX3 expression and activity / ganglioside metabolic process / regulation of binding / regulation of DNA binding / positive regulation of microglia differentiation / negative regulation of skeletal muscle tissue development / regulation of striated muscle tissue development / regulation of protein import into nucleus / type III transforming growth factor beta receptor binding / Langerhans cell differentiation / negative regulation of hyaluronan biosynthetic process / extracellular matrix assembly / negative regulation of macrophage cytokine production / integrin alphav-beta6 complex / integrin alphav-beta8 complex / hard palate development / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / odontoblast differentiation / integrin alphav-beta5 complex / : / opsonin binding / positive regulation of isotype switching to IgA isotypes / integrin alphav-beta1 complex / membrane protein intracellular domain proteolysis / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / hyaluronan catabolic process / regulation of transforming growth factor beta receptor signaling pathway / ATP biosynthetic process / Laminin interactions / receptor catabolic process / placenta blood vessel development / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / type II transforming growth factor beta receptor binding / alphav-beta3 integrin-PKCalpha complex / entry into host cell by a symbiont-containing vacuole / positive regulation of chemotaxis / type I transforming growth factor beta receptor binding / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / negative regulation of myoblast differentiation / negative regulation of low-density lipoprotein receptor activity / cell-cell junction organization / regulation of phagocytosis / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / response to cholesterol / transforming growth factor beta binding / filopodium membrane / positive regulation of small GTPase mediated signal transduction / extracellular matrix binding / positive regulation of fibroblast migration / phosphate-containing compound metabolic process / apolipoprotein A-I-mediated signaling pathway / cartilage development / apoptotic cell clearance / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / integrin complex / Molecules associated with elastic fibres / positive regulation of intracellular signal transduction / positive regulation of epidermal growth factor receptor signaling pathway / microvillus membrane / cell adhesion mediated by integrin / negative chemotaxis / Syndecan interactions / negative regulation of cell-cell adhesion / negative regulation of fat cell differentiation / cell-substrate adhesion / positive regulation of interleukin-17 production / endodermal cell differentiation / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / positive regulation of SMAD protein signal transduction / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / negative regulation of blood vessel endothelial cell migration / positive regulation of cell division / fibronectin binding / negative regulation of cell cycle / positive regulation of cell adhesion / ECM proteoglycans / positive regulation of collagen biosynthetic process / voltage-gated calcium channel activity / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / vasculogenesis Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||||||||
Authors | Campbell, M.G. / Cormier, A. / Cheng, Y. / Nishimura, S.L. | ||||||||||||||||||||||||
Funding support | United States, 7items
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Citation | Journal: Cell / Year: 2020 Title: Cryo-EM Reveals Integrin-Mediated TGF-β Activation without Release from Latent TGF-β. Authors: Melody G Campbell / Anthony Cormier / Saburo Ito / Robert I Seed / Andrew J Bondesson / Jianlong Lou / James D Marks / Jody L Baron / Yifan Cheng / Stephen L Nishimura / Abstract: Integrin αvβ8 binds with exquisite specificity to latent transforming growth factor-β (L-TGF-β). This binding is essential for activating L-TGF-β presented by a variety of cell types. ...Integrin αvβ8 binds with exquisite specificity to latent transforming growth factor-β (L-TGF-β). This binding is essential for activating L-TGF-β presented by a variety of cell types. Inhibiting αvβ8-mediated TGF-β activation blocks immunosuppressive regulatory T cell differentiation, which is a potential therapeutic strategy in cancer. Using cryo-electron microscopy, structure-guided mutagenesis, and cell-based assays, we reveal the binding interactions between the entire αvβ8 ectodomain and its intact natural ligand, L-TGF-β, as well as two different inhibitory antibody fragments to understand the structural underpinnings of αvβ8 binding specificity and TGF-β activation. Our studies reveal a mechanism of TGF-β activation where mature TGF-β signals within the confines of L-TGF-β and the release and diffusion of TGF-β are not required. The structural details of this mechanism provide a rational basis for therapeutic strategies to inhibit αvβ8-mediated L-TGF-β activation. | ||||||||||||||||||||||||
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 | 6uja.cif.gz | 241.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uja.ent.gz | 176 KB | Display | PDB format |
PDBx/mmJSON format | 6uja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uja_validation.pdf.gz | 993.3 KB | Display | wwPDB validaton report |
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Full document | 6uja_full_validation.pdf.gz | 996.2 KB | Display | |
Data in XML | 6uja_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 6uja_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/6uja ftp://data.pdbj.org/pub/pdb/validation_reports/uj/6uja | HTTPS FTP |
-Related structure data
Related structure data | 20794MC 6ujbC 6ujcC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10343 (Title: CryoEM dataset containing multiple conformations of the asymmetric αVβ8 integrin bound to latent TGF-β on a holey carbon grid (strongly preferred orientations) Data size: 1.2 TB Data #1: Unaligned 80-frame movies of αVβ8 integrin bound to latent TGF-β on a holey carbon grid [micrographs - multiframe] Data #2: Dose-weighted aligned micrographs of αVβ8 integrin bound to latent TGF-β on a holey carbon grid [micrographs - single frame] Data #3: Dose-weighted aligned particle stacks of αVβ8 integrin bound to latent TGF-β on a holey carbon grid [picked particles - single frame - processed]) EMPIAR-10344 (Title: CryoEM dataset containing multiple conformations of the asymmetric αVβ8 integrin bound to latent TGF-β on a graphene oxide grid (preferred orientations) Data size: 2.2 TB Data #1: Unaligned 80-frame movies of αVβ8 integrin bound to latent TGF-β on a graphene oxide grid [micrographs - multiframe] Data #2: Dose-weighted aligned micrographs of αVβ8 integrin bound to latent TGF-β on a graphene oxide grid [micrographs - single frame] Data #3: Dose-weighted aligned particle stacks of αVβ8 integrin bound to latent TGF-β on a graphene oxide grid [picked particles - single frame - processed]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules ABD
#1: Protein | Mass: 112813.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA, VTNR / Cell line (production host): CHO lec 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): ovary / References: UniProt: P06756 |
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#2: Protein | Mass: 81276.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB8 / Cell line (production host): CHO lec 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): ovary / References: UniProt: P26012 |
#3: Protein | Mass: 41434.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: TGFB1 / Cell line (production host): HEK293A / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: P07200 |
-Sugars , 3 types, 8 molecules
#4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #7: Sugar | |
-Non-polymers , 2 types, 6 molecules
#6: Chemical | ChemComp-CA / #8: Chemical | ChemComp-MG / | |
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-Details
Compound details | LTGFb is a homodimer in the sample, but only a single chain (chain D) is modeled. |
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Has ligand of interest | N |
-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 |
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Molecular weight | Value: 0.26 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: GRAPHENE OXIDE | ||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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 | Electron dose: 70 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43600 / Symmetry type: POINT |