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Yorodumi- PDB-2wuh: Crystal structure of the DDR2 discoidin domain bound to a triple-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wuh | ||||||
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Title | Crystal structure of the DDR2 discoidin domain bound to a triple- helical collagen peptide | ||||||
Components |
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Keywords | RECEPTOR/PEPTIDE / RECEPTOR-PEPTIDE COMPLEX / TRANSFERASE / NUCLEOTIDE-BINDING / TYROSINE-PROTEIN KINASE | ||||||
Function / homology | Function and homology information positive regulation of hepatic stellate cell proliferation / protein tyrosine kinase collagen receptor activity / biomineral tissue development / positive regulation of extracellular matrix disassembly / chondrocyte proliferation / positive regulation of hepatic stellate cell activation / endochondral bone growth / regulation of extracellular matrix disassembly / negative regulation of hydrogen peroxide-mediated programmed cell death / collagen-activated tyrosine kinase receptor signaling pathway ...positive regulation of hepatic stellate cell proliferation / protein tyrosine kinase collagen receptor activity / biomineral tissue development / positive regulation of extracellular matrix disassembly / chondrocyte proliferation / positive regulation of hepatic stellate cell activation / endochondral bone growth / regulation of extracellular matrix disassembly / negative regulation of hydrogen peroxide-mediated programmed cell death / collagen-activated tyrosine kinase receptor signaling pathway / regulation of bone mineralization / positive regulation of fibroblast migration / cellular response to angiotensin / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / regulation of tissue remodeling / positive regulation of wound healing / positive regulation of G1/S transition of mitotic cell cycle / Non-integrin membrane-ECM interactions / positive regulation of collagen biosynthetic process / positive regulation of protein kinase activity / transmembrane receptor protein tyrosine kinase activity / positive regulation of osteoblast differentiation / ossification / cellular response to transforming growth factor beta stimulus / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / response to muscle stretch / receptor protein-tyrosine kinase / positive regulation of DNA-binding transcription factor activity / peptidyl-tyrosine phosphorylation / positive regulation of neuron projection development / positive regulation of fibroblast proliferation / actin cytoskeleton / cellular response to hypoxia / protein autophosphorylation / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / focal adhesion / negative regulation of apoptotic process / signal transduction / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Carafoli, F. / Bihan, D. / Stathopoulos, S. / Konitsiotis, A.D. / Kvansakul, M. / Farndale, R.W. / Leitinger, B. / Hohenester, E. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Crystallographic Insight Into Collagen Recognition by Discoidin Domain Receptor 2 Authors: Carafoli, F. / Bihan, D. / Stathopoulos, S. / Konitsiotis, A.D. / Kvansakul, M. / Farndale, R.W. / Leitinger, B. / Hohenester, E. #1: Journal: Embo J. / Year: 2007 Title: Structural Basis of the Collagen-Binding Mode of Discoidin Domain Receptor 2. Authors: Ichikawa, O. / Osawa, M. / Nishida, N. / Goshima, N. / Nomura, N. / Shimada, I. #2: Journal: J.Biol.Chem. / Year: 2008 Title: Characterization of High Affinity Binding Motifs for the Discoidin Domain Receptor Ddr2 in Collagen. Authors: Konitsiotis, A.D. / Raynal, N. / Bihan, D. / Hohenester, E. / Farndale, R.W. / Leitinger, B. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wuh.cif.gz | 65 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wuh.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wuh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wuh_validation.pdf.gz | 459.2 KB | Display | wwPDB validaton report |
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Full document | 2wuh_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 2wuh_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 2wuh_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/2wuh ftp://data.pdbj.org/pub/pdb/validation_reports/wu/2wuh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20108.637 Da / Num. of mol.: 1 / Fragment: DISCOIDIN DOMAIN, RESIDUES 26-190 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: Q16832 | ||||
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#2: Protein/peptide | Mass: 2633.847 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: ACETYLATED N-TERMINUS / Source: (synth.) HOMO SAPIENS (human) #3: Water | ChemComp-HOH / | Nonpolymer details | ACETYL GROUP (ACE): ACETYLATED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40.85 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 |
Detector | Detector: CCD / Date: Dec 16, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 27359 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.3 / % possible all: 67.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2QQJ AND 2V53 Resolution: 1.6→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.2491 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.61 Å / Total num. of bins used: 50 /
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Xplor file |
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