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Yorodumi- PDB-1mse: SOLUTION STRUCTURE OF A SPECIFIC DNA COMPLEX OF THE MYB DNA-BINDI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mse | ||||||
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Title | SOLUTION STRUCTURE OF A SPECIFIC DNA COMPLEX OF THE MYB DNA-BINDING DOMAIN WITH COOPERATIVE RECOGNITION HELICES | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / DNA / DOUBLE HELIX / C-MYB DNA-BINDING DOMAIN / PROTOONCOGENE PRODUCT / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
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 / G1/S transition of mitotic cell cycle / RNA polymerase II transcription regulator complex / 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 / ENERGY MINIMIZATION | ||||||
Authors | Ogata, K. / Morikawa, S. / Nakamura, H. / Sekikawa, A. / Inoue, T. / Kanai, H. / Sarai, A. / Ishii, S. / Nishimura, Y. | ||||||
Citation | 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. #1: 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 | 1mse.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mse.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 1mse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mse_validation.pdf.gz | 251.7 KB | Display | wwPDB validaton report |
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Full document | 1mse_full_validation.pdf.gz | 251.5 KB | Display | |
Data in XML | 1mse_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 1mse_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/1mse ftp://data.pdbj.org/pub/pdb/validation_reports/ms/1mse | 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: DNA chain | Mass: 4811.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID |
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#2: DNA chain | Mass: 4984.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID |
#3: Protein | Mass: 12676.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PAR2156NCO1R23 / Production host: Escherichia coli (E. coli) / Keywords: POLYPEPTIDE / References: UniProt: P06876 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: THE STRUCTURES OF N- AND C-TERMINI OF THE PEPTIDE CHAIN (MET 89 - PRO 94 AND ASN 186 - VAL 193) WERE DISORDERED AMONG THE 25 STRUCTURES. THE ORIENTATION OF THE LAST 5 BASE PAIRS OF THE DNA IS ...Text: THE STRUCTURES OF N- AND C-TERMINI OF THE PEPTIDE CHAIN (MET 89 - PRO 94 AND ASN 186 - VAL 193) WERE DISORDERED AMONG THE 25 STRUCTURES. THE ORIENTATION OF THE LAST 5 BASE PAIRS OF THE DNA IS POORLY DEFINED WITH RESPECT TO THE CORE OF THE COMPLEX. CONSEQUENTLY, ONLY THE COORDINATES OF BASE PAIRS 1 - 11 OF DNA HAVE BEEN DEPOSITED TOGETHER WITH THOSE OF THE PROTEIN IN THE COMPLEX. |
-Sample preparation
Sample conditions | pH: 6.8 / Temperature: 310 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-Processing
Software | Name: AMBER / Classification: refinement | |||||||||
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NMR software |
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Refinement | Method: ENERGY MINIMIZATION / Software ordinal: 1 Details: RMSD BOND DISTANCES 0.006 ANGSTROMS RMSD BOND ANGLES 0.857 DEGREES RMSD CHIRAL CENTERS 0.0664 ANGSTROMS NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 1815 NUMBER OF NUCLEIC ...Details: RMSD BOND DISTANCES 0.006 ANGSTROMS RMSD BOND ANGLES 0.857 DEGREES RMSD CHIRAL CENTERS 0.0664 ANGSTROMS NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 1815 NUMBER OF NUCLEIC ACID ATOMS 698 AMBER FORCE FIELD | |||||||||
NMR constraints | NOE constraints total: 1732 / Hydrogen bond constraints total count: 350 | |||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 25 / Conformers submitted total number: 1 |