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

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Entry
Database: PDB / ID: 1msf
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 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
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:
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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)25 / -
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
#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
#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 (VECTOR:PAR2156NCO1) / Production host: Escherichia coli (E. coli) / References: UniProt: P06876

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

SoftwareName: AMBER / Classification: refinement
NMR ensembleConformers submitted total number: 25

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