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Yorodumi- PDB-1m3b: Solution structure of a circular form of the N-terminal SH3 domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m3b | ||||||
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Title | Solution structure of a circular form of the N-terminal SH3 domain (A134C, E135G, R191G mutant) from oncogene protein c-Crk. | ||||||
Components | Proto-oncogene C-crk | ||||||
Keywords | PROTEIN BINDING / SH3 / SH3 DOMAIN / CIRCULAR PROTEIN / CYCLIZED PROTEIN / ADAPTOR PROTEIN | ||||||
Function / homology | Function and homology information PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / regulation of leukocyte migration ...PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / regulation of leukocyte migration / Downstream signal transduction / postsynaptic specialization assembly / protein phosphorylated amino acid binding / response to peptide / regulation of T cell migration / p130Cas linkage to MAPK signaling for integrins / reelin-mediated signaling pathway / regulation of dendrite development / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of natural killer cell mediated cytotoxicity / response to yeast / Regulation of signaling by CBL / Regulation of actin dynamics for phagocytic cup formation / regulation of Rac protein signal transduction / negative regulation of wound healing / negative regulation of cell motility / protein localization to membrane / VEGFA-VEGFR2 Pathway / cellular response to nitric oxide / cellular response to insulin-like growth factor stimulus / establishment of cell polarity / regulation of GTPase activity / enzyme-linked receptor protein signaling pathway / positive regulation of smooth muscle cell migration / dendrite development / positive regulation of Rac protein signal transduction / regulation of cell adhesion mediated by integrin / ephrin receptor signaling pathway / signaling adaptor activity / positive regulation of substrate adhesion-dependent cell spreading / cellular response to transforming growth factor beta stimulus / insulin-like growth factor receptor binding / cytoskeletal protein binding / ephrin receptor binding / phosphotyrosine residue binding / SH2 domain binding / cell chemotaxis / protein tyrosine kinase binding / cellular response to nerve growth factor stimulus / hippocampus development / lipid metabolic process / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / neuron migration / response to hydrogen peroxide / neuromuscular junction / receptor tyrosine kinase binding / cerebral cortex development / SH3 domain binding / actin cytoskeleton / signaling receptor complex adaptor activity / cell migration / protein-macromolecule adaptor activity / regulation of cell shape / actin cytoskeleton organization / scaffold protein binding / cell population proliferation / protein domain specific binding / ubiquitin protein ligase binding / enzyme binding / protein-containing complex / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / Simulated annealing, torsion angle dynamics | ||||||
Authors | Schumann, F.H. / Varadan, R. / Tayakuniyil, P.P. / Hall, J.B. / Camarero, J.A. / Fushman, D. | ||||||
Citation | Journal: To be Published Title: Changing protein backbone topology: Structural and dynamic consequences of the backbone cyclization in SH3 domain Authors: Schumann, F.H. / Varadan, R. / Tayakuniyil, P.P. / Hall, J.B. / Camarero, J.A. / Fushman, D. #1: Journal: J.Mol.Biol. / Year: 2001 Title: Rescuing a destabilized protein fold through backbone cyclization Authors: Camarero, J.A. / Fushman, D. / Sato, S. / Giriat, I. / Cowburn, D. / Raleigh, D.P. / Muir, T.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m3b.cif.gz | 361.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m3b.ent.gz | 311 KB | Display | PDB format |
PDBx/mmJSON format | 1m3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m3b_validation.pdf.gz | 341.8 KB | Display | wwPDB validaton report |
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Full document | 1m3b_full_validation.pdf.gz | 499.3 KB | Display | |
Data in XML | 1m3b_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 1m3b_validation.cif.gz | 41.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/1m3b ftp://data.pdbj.org/pub/pdb/validation_reports/m3/1m3b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6831.592 Da / Num. of mol.: 1 / Fragment: N-TERMINAL SH3 DOMAIN (residues 134-191) / Mutation: R191G, E135G, A134C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: CRK / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q64010 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques combined with 2D 1H-15N HSQC data. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 100 mM NaCl / pH: 7.2 / Pressure: ambient / Temperature: 307 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: The structures are based on 1151 restraints, 1054 are NOE-derived distance contraints, 25 dihedral angle constraints, and 72 distance restraints from hydrogen bonds. Structures were ...Details: The structures are based on 1151 restraints, 1054 are NOE-derived distance contraints, 25 dihedral angle constraints, and 72 distance restraints from hydrogen bonds. Structures were calculated using program DYANA. No further refinement was performed. | ||||||||||||||||||||
NMR representative | Selection criteria: lowest target function | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest target function Conformers calculated total number: 200 / Conformers submitted total number: 20 |