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Yorodumi- PDB-1idy: STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, MINIMIZED AVERAGE STR... -
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-Basic information
Entry | Database: PDB / ID: 1idy | ||||||
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Title | STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE | ||||||
Components | MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3 | ||||||
Keywords | DNA BINDING PROTEIN / PROTOONCOGENE PRODUCT / DNA-BINDING PROTEIN | ||||||
Function / homology | Function and homology information positive regulation of testosterone secretion / myeloid cell development / positive regulation of hepatic stellate cell proliferation / positive regulation of hepatic stellate cell activation / positive regulation of transforming growth factor beta production / embryonic digestive tract development / stem cell division / myeloid cell differentiation / cellular response to interleukin-6 / WD40-repeat domain binding ...positive regulation of testosterone secretion / myeloid cell development / positive regulation of hepatic stellate cell proliferation / positive regulation of hepatic stellate cell activation / positive regulation of transforming growth factor beta production / embryonic digestive tract development / stem cell division / myeloid cell differentiation / cellular response to interleukin-6 / WD40-repeat domain binding / homeostasis of number of cells / positive regulation of collagen biosynthetic process / positive regulation of glial cell proliferation / spleen development / B cell differentiation / thymus development / cellular response to leukemia inhibitory factor / positive regulation of smooth muscle cell proliferation / RNA polymerase II transcription regulator complex / G1/S transition of mitotic cell cycle / calcium ion transport / positive regulation of neuron apoptotic process / mitotic cell cycle / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING IN 4D | ||||||
Authors | Furukawa, K. / Oda, M. / Nakamura, H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: A small engineered protein lacks structural uniqueness by increasing the side-chain conformational entropy. Authors: Furukawa, K. / Oda, M. / Nakamura, H. #1: Journal: Nat.Struct.Biol. / Year: 1995 Title: Comparison of the Free and DNA-Complexed Forms of the DNA-Binding Domain from C-Myb Authors: Ogata, K. / Morikawa, S. / Nakamura, H. / Hojo, H. / Yoshimura, S. / Zhang, R. / Aimoto, S. / Ametani, Y. / Hirata, Z. / Sarai, A. / al., et #2: Journal: Cell(Cambridge,Mass.) / Year: 1994 Title: Solution Structure of a Specific DNA Complex of the Myb DNA-Binding Domain with Cooperative Recognition Helices Authors: Ogata, K. / Morikawa, S. / Nakamura, H. / Sekikawa, A. / Inoue, T. / Kanai, H. / Sarai, A. / Ishii, S. / Nishimura, Y. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: Solution Structure of a DNA-Binding Unit of Myb: A Helix-Turn-Helix-Related Motif with Conserved Tryptophans Forming a Hydrophobic Core Authors: Ogata, K. / Hojo, H. / Aimoto, S. / Nakai, T. / Nakamura, H. / Sarai, A. / Ishii, S. / Nishimura, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1idy.cif.gz | 28.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1idy.ent.gz | 18.2 KB | Display | PDB format |
PDBx/mmJSON format | 1idy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1idy ftp://data.pdbj.org/pub/pdb/validation_reports/id/1idy | HTTPS FTP |
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-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: 6521.496 Da / Num. of mol.: 1 / Mutation: P140M, I155L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PRP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P06876 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D 1H-1H NOESY |
-Sample preparation
Sample conditions | pH: 5 / Temperature: 283 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX 600 / Manufacturer: Bruker / Model: AMX 600 / Field strength: 600.13 MHz |
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-Processing
Software | Name: AMBER / Classification: refinement | |||||||||
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NMR software |
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Refinement | Method: SIMULATED ANNEALING IN 4D / Software ordinal: 1 | |||||||||
NMR ensemble | Conformer selection criteria: 0.1 ANGSTROM MAXIMUM DISTANCE VIOLATION Conformers calculated total number: 120 / Conformers submitted total number: 1 |