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- PDB-1mse: SOLUTION STRUCTURE OF A SPECIFIC DNA COMPLEX OF THE MYB DNA-BINDI... -

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Entry
Database: PDB / ID: 1mse
TitleSOLUTION STRUCTURE OF A SPECIFIC DNA COMPLEX OF THE MYB DNA-BINDING DOMAIN WITH COOPERATIVE RECOGNITION HELICES
Components
  • C-Myb DNA-Binding Domain
  • DNA (5'-D(*AP*TP*GP*TP*GP*TP*GP*TP*CP*AP*GP*TP*TP*AP*GP*G)-3')
  • DNA (5'-D(*CP*CP*TP*AP*AP*CP*TP*GP*AP*CP*AP*CP*AP*CP*AP*T)-3')
KeywordsDNA 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 / positive regulation of hepatic stellate cell proliferation / myeloid cell development / positive regulation of transforming growth factor beta production / positive regulation of hepatic stellate cell activation / negative regulation of hematopoietic progenitor cell differentiation / skeletal muscle cell proliferation / embryonic digestive tract development / myeloid cell differentiation / cellular response to interleukin-6 ...positive regulation of testosterone secretion / positive regulation of hepatic stellate cell proliferation / myeloid cell development / positive regulation of transforming growth factor beta production / positive regulation of hepatic stellate cell activation / negative regulation of hematopoietic progenitor cell differentiation / skeletal muscle cell proliferation / embryonic digestive tract development / myeloid cell differentiation / cellular response to interleukin-6 / T-helper 2 cell differentiation / WD40-repeat domain binding / stem cell division / positive regulation of collagen biosynthetic process / homeostasis of number of cells / positive regulation of glial cell proliferation / negative regulation of megakaryocyte differentiation / spleen development / cellular response to retinoic acid / positive regulation of smooth muscle cell proliferation / thymus development / cellular response to leukemia inhibitory factor / B cell differentiation / response to ischemia / erythrocyte differentiation / G1/S transition of mitotic cell cycle / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / cellular response to hydrogen peroxide / calcium ion transport / positive regulation of neuron apoptotic process / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / response to hypoxia / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Homeodomain-like ...Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Homeodomain-like / SANT/Myb domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional activator Myb
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / ENERGY MINIMIZATION
AuthorsOgata, 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
DepositionJan 24, 1995Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*TP*AP*AP*CP*TP*GP*AP*CP*AP*CP*AP*CP*AP*T)-3')
B: DNA (5'-D(*AP*TP*GP*TP*GP*TP*GP*TP*CP*AP*GP*TP*TP*AP*GP*G)-3')
C: C-Myb DNA-Binding Domain


Theoretical massNumber of molelcules
Total (without water)22,4723
Polymers22,4723
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 25structures with the least restraint violations,structures with the lowest energy
Representative

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Components

#1: DNA chain DNA (5'-D(*CP*CP*TP*AP*AP*CP*TP*GP*AP*CP*AP*CP*AP*CP*AP*T)-3')


Mass: 4811.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#2: DNA chain DNA (5'-D(*AP*TP*GP*TP*GP*TP*GP*TP*CP*AP*GP*TP*TP*AP*GP*G)-3')


Mass: 4984.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#3: Protein C-Myb DNA-Binding Domain


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: 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.

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Sample preparation

Sample conditionspH: 6.8 / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameDeveloperClassification
EMBOSST. NAKAI, A. KIDERA, H. NAKAMURAstructure solution
PRESTOMORIKAMI,NAKAI,KIDERA,SAITO,NAKAMURArefinement
RefinementMethod: 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 constraintsNOE constraints total: 1732 / Hydrogen bond constraints total count: 350
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 1

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