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Yorodumi- PDB-5l0q: Crystal structure of the complex between ADAM10 D+C domain and a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l0q | ||||||
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Title | Crystal structure of the complex between ADAM10 D+C domain and a conformation specific mAb 8C7. | ||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / ADAM protease / mAb / 8C7 / Notch signaling / therapeutic antibody / cancer stem cell / drug resistance / HYDROLASE-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information Degradation of the extracellular matrix / ADAM10 endopeptidase / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / negative regulation of cell adhesion / clathrin-coated vesicle / Neutrophil degranulation / Golgi-associated vesicle / amyloid precursor protein catabolic process ...Degradation of the extracellular matrix / ADAM10 endopeptidase / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / negative regulation of cell adhesion / clathrin-coated vesicle / Neutrophil degranulation / Golgi-associated vesicle / amyloid precursor protein catabolic process / membrane protein ectodomain proteolysis / Notch signaling pathway / synaptic membrane / adherens junction / protein processing / metalloendopeptidase activity / SH3 domain binding / metallopeptidase activity / endopeptidase activity / in utero embryonic development / protein phosphorylation / Golgi membrane / axon / dendrite / protein kinase binding / Golgi apparatus / cell surface / protein homodimerization activity / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.759 Å | ||||||
Authors | Xu, K. / Saha, N. / Nikolov, D.B. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2016 Title: An activated form of ADAM10 is tumor selective and regulates cancer stem-like cells and tumor growth. Authors: Atapattu, L. / Saha, N. / Chheang, C. / Eissman, M.F. / Xu, K. / Vail, M.E. / Hii, L. / Llerena, C. / Liu, Z. / Horvay, K. / Abud, H.E. / Kusebauch, U. / Moritz, R.L. / Ding, B.S. / Cao, Z. ...Authors: Atapattu, L. / Saha, N. / Chheang, C. / Eissman, M.F. / Xu, K. / Vail, M.E. / Hii, L. / Llerena, C. / Liu, Z. / Horvay, K. / Abud, H.E. / Kusebauch, U. / Moritz, R.L. / Ding, B.S. / Cao, Z. / Rafii, S. / Ernst, M. / Scott, A.M. / Nikolov, D.B. / Lackmann, M. / Janes, P.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l0q.cif.gz | 259.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l0q.ent.gz | 207.1 KB | Display | PDB format |
PDBx/mmJSON format | 5l0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l0q_validation.pdf.gz | 524.4 KB | Display | wwPDB validaton report |
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Full document | 5l0q_full_validation.pdf.gz | 544.5 KB | Display | |
Data in XML | 5l0q_validation.xml.gz | 50.1 KB | Display | |
Data in CIF | 5l0q_validation.cif.gz | 70.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/5l0q ftp://data.pdbj.org/pub/pdb/validation_reports/l0/5l0q | HTTPS FTP |
-Related structure data
Related structure data | 2ao7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules BECF
#2: Antibody | Mass: 23712.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 23930.732 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Protein / Sugars , 2 types, 6 molecules AD
#1: Protein | Mass: 21780.699 Da / Num. of mol.: 2 / Fragment: UNP residues 455-646 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ADAM10, MADM / Production host: Homo sapiens (human) / References: UniProt: Q10741, ADAM10 endopeptidase #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 349 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES, 0.2M NaCl, and 1.6 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.759→125.262 Å / Num. all: 52855 / Num. obs: 52855 / % possible obs: 99.1 % / Redundancy: 4.4 % / Rpim(I) all: 0.071 / Rrim(I) all: 0.155 / Rsym value: 0.125 / Net I/av σ(I): 5.556 / Net I/σ(I): 10.3 / Num. measured all: 234255 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AO7 Resolution: 2.759→125.262 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.759→125.262 Å
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Refine LS restraints |
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LS refinement shell |
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