+Open data
-Basic information
Entry | Database: PDB / ID: 8esv | |||||||||
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Title | Structure of human ADAM10-Tspan15 complex bound to 11G2 vFab | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Protease / Metalloprotease / Tetraspanin / Sheddase / Adhesion | |||||||||
Function / homology | Function and homology information regulation of membrane protein ectodomain proteolysis / constitutive protein ectodomain proteolysis / ADAM10 endopeptidase / regulation of vasculature development / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / protein catabolic process at postsynapse / postsynapse organization / pore complex assembly ...regulation of membrane protein ectodomain proteolysis / constitutive protein ectodomain proteolysis / ADAM10 endopeptidase / regulation of vasculature development / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / protein catabolic process at postsynapse / postsynapse organization / pore complex assembly / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / regulation of Notch signaling pathway / perinuclear endoplasmic reticulum / positive regulation of T cell chemotaxis / tetraspanin-enriched microdomain / NOTCH4 Activation and Transmission of Signal to the Nucleus / metallodipeptidase activity / negative regulation of cell adhesion / adherens junction organization / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / clathrin-coated vesicle / regulation of postsynapse organization / Golgi-associated vesicle / cochlea development / Signaling by EGFR / negative regulation of Notch signaling pathway / pore complex / amyloid precursor protein catabolic process / tertiary granule membrane / membrane protein ectodomain proteolysis / protein maturation / Collagen degradation / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / response to tumor necrosis factor / specific granule membrane / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Degradation of the extracellular matrix / Activated NOTCH1 Transmits Signal to the Nucleus / synaptic membrane / protein localization to plasma membrane / NOTCH3 Activation and Transmission of Signal to the Nucleus / integrin-mediated signaling pathway / adherens junction / Post-translational protein phosphorylation / protein processing / metalloendopeptidase activity / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SH3 domain binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / integrin binding / cell junction / cell-cell signaling / late endosome membrane / positive regulation of cell growth / endopeptidase activity / in utero embryonic development / molecular adaptor activity / postsynaptic density / nuclear body / positive regulation of cell migration / Amyloid fiber formation / endoplasmic reticulum lumen / axon / Golgi membrane / protein phosphorylation / negative regulation of gene expression / intracellular membrane-bounded organelle / focal adhesion / signaling receptor binding / glutamatergic synapse / dendrite / positive regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / Golgi apparatus / enzyme binding / cell surface / protein homodimerization activity / extracellular exosome / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Lipper, C.H. / Blacklow, S.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell / Year: 2023 Title: Structural basis for membrane-proximal proteolysis of substrates by ADAM10. Authors: Colin H Lipper / Emily D Egan / Khal-Hentz Gabriel / Stephen C Blacklow / Abstract: The endopeptidase ADAM10 is a critical catalyst for the regulated proteolysis of key drivers of mammalian development, physiology, and non-amyloidogenic cleavage of APP as the primary α-secretase. ...The endopeptidase ADAM10 is a critical catalyst for the regulated proteolysis of key drivers of mammalian development, physiology, and non-amyloidogenic cleavage of APP as the primary α-secretase. ADAM10 function requires the formation of a complex with a C8-tetraspanin protein, but how tetraspanin binding enables positioning of the enzyme active site for membrane-proximal cleavage remains unknown. We present here a cryo-EM structure of a vFab-ADAM10-Tspan15 complex, which shows that Tspan15 binding relieves ADAM10 autoinhibition and acts as a molecular measuring stick to position the enzyme active site about 20 Å from the plasma membrane for membrane-proximal substrate cleavage. Cell-based assays of N-cadherin shedding establish that the positioning of the active site by the interface between the ADAM10 catalytic domain and the bound tetraspanin influences selection of the preferred cleavage site. Together, these studies reveal the molecular mechanism underlying ADAM10 proteolysis at membrane-proximal sites and offer a roadmap for its modulation in disease. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8esv.cif.gz | 206.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8esv.ent.gz | 153.8 KB | Display | PDB format |
PDBx/mmJSON format | 8esv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8esv_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8esv_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8esv_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 8esv_validation.cif.gz | 57.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/8esv ftp://data.pdbj.org/pub/pdb/validation_reports/es/8esv | HTTPS FTP |
-Related structure data
Related structure data | 28580MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 60477.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM10, KUZ, MADM / Plasmid: pRK5M / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: O14672, ADAM10 endopeptidase |
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#2: Protein | Mass: 34740.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TSPAN15, NET7, TM4SF15, UNQ677/PRO1311 / Plasmid: pcDNA3.1/Hygro(+) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: O95858 |
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 24135.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pFUSE-hIgG1-Fc2 Details (production host): Heavy and light chain in same vector with P2A sequence Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
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#4: Antibody | Mass: 24185.803 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pFUSE-hIgG1-Fc2 Details (production host): Heavy and light chain in same vector with P2A sequence Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
-Sugars , 3 types, 3 molecules
#5: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-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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#6: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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 |
#7: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 5 molecules
#8: Chemical | ChemComp-CA / |
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#9: Chemical | ChemComp-ZN / |
#10: Chemical | ChemComp-BAT / |
#11: Chemical |
-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
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Molecular weight | 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.: 2.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse | |||||||||||||||||||||||||
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 7 seconds with a blot force of 15 |
-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: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.3 sec. / Electron dose: 51.99 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10037 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178031 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL |