+Open data
-Basic information
Entry | Database: PDB / ID: 8snl | ||||||
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Title | Structure of human ADAM17/iRhom2 sheddase complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/HYDROLASE / Membrane protein complex / MEMBRANE PROTEIN / MEMBRANE PROTEIN-HYDROLASE complex | ||||||
Function / homology | Function and homology information ADAM 17 endopeptidase / regulation of mast cell apoptotic process / signal release / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / regulation of epidermal growth factor receptor signaling pathway / cellular response to high density lipoprotein particle stimulus / positive regulation of epidermal growth factor-activated receptor activity / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / interleukin-6 receptor binding / Notch receptor processing ...ADAM 17 endopeptidase / regulation of mast cell apoptotic process / signal release / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / regulation of epidermal growth factor receptor signaling pathway / cellular response to high density lipoprotein particle stimulus / positive regulation of epidermal growth factor-activated receptor activity / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / interleukin-6 receptor binding / Notch receptor processing / tumor necrosis factor binding / protein transporter activity / positive regulation of T cell chemotaxis / TNF signaling / Signaling by EGFR / positive regulation of leukocyte chemotaxis / germinal center formation / Release of Hh-Np from the secreting cell / Regulated proteolysis of p75NTR / commissural neuron axon guidance / positive regulation of tumor necrosis factor-mediated signaling pathway / neutrophil mediated immunity / positive regulation of cyclin-dependent protein serine/threonine kinase activity / wound healing, spreading of epidermal cells / negative regulation of cold-induced thermogenesis / Notch binding / CD163 mediating an anti-inflammatory response / positive regulation of vascular endothelial cell proliferation / cell adhesion mediated by integrin / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of G1/S transition of mitotic cell cycle / regulation of protein secretion / growth factor binding / amyloid precursor protein catabolic process / cytokine binding / Collagen degradation / membrane protein ectodomain proteolysis / positive regulation of blood vessel endothelial cell migration / negative regulation of protein secretion / Growth hormone receptor signaling / positive regulation of chemokine production / Nuclear signaling by ERBB4 / spleen development / negative regulation of inflammatory response to antigenic stimulus / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / Activated NOTCH1 Transmits Signal to the Nucleus / B cell differentiation / negative regulation of transforming growth factor beta receptor signaling pathway / protein localization to plasma membrane / PDZ domain binding / cell motility / protein processing / metalloendopeptidase activity / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SH3 domain binding / Golgi lumen / integrin binding / metallopeptidase activity / positive regulation of tumor necrosis factor production / actin cytoskeleton / protein transport / peptidase activity / positive regulation of cell growth / endopeptidase activity / T cell differentiation in thymus / response to lipopolysaccharide / response to hypoxia / cell adhesion / positive regulation of cell migration / defense response to Gram-positive bacterium / apical plasma membrane / response to xenobiotic stimulus / membrane raft / Golgi membrane / endoplasmic reticulum lumen / positive regulation of cell population proliferation / endoplasmic reticulum membrane / cell surface / proteolysis / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å | ||||||
Authors | Zhao, H. / Dai, Y. / Wang, Y. / Lee, C.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure of human ADAM17/iRhom2 sheddase complex Authors: Zhao, H. / Dai, Y. / Wang, Y. / Lee, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8snl.cif.gz | 221.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8snl.ent.gz | 170 KB | Display | PDB format |
PDBx/mmJSON format | 8snl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8snl_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8snl_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8snl_validation.xml.gz | 45.7 KB | Display | |
Data in CIF | 8snl_validation.cif.gz | 66.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/8snl ftp://data.pdbj.org/pub/pdb/validation_reports/sn/8snl | HTTPS FTP |
-Related structure data
Related structure data | 40628MC 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
#1: Protein | Mass: 93141.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM17, CSVP, TACE / Production host: Homo sapiens (human) / References: UniProt: P78536, ADAM 17 endopeptidase |
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#2: Protein | Mass: 93503.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RHBDF2, IRHOM2, RHBDL5, RHBDL6 / Production host: Homo sapiens (human) / References: UniProt: Q6PJF5 |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-CA / |
Has ligand of interest | Y |
-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: human ADAM17/iRhom2 sheddase complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 79.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.18.2_3874: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 229986 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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