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- PDB-1idy: STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, MINIMIZED AVERAGE STR... -

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Basic information

Entry
Database: PDB / ID: 1idy
TitleSTRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsMOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3
KeywordsDNA 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 / 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
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 / SANT/Myb domain / 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 / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional activator Myb
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / SIMULATED ANNEALING IN 4D
AuthorsFurukawa, 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
DepositionAug 15, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type / _pdbx_database_related.details / _pdbx_database_status.process_site / _struct_keywords.text / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3


Theoretical massNumber of molelcules
Total (without water)6,5211
Polymers6,5211
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1200.1 ANGSTROM MAXIMUM DISTANCE VIOLATION
Representative

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Components

#1: Protein MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

Sample conditionspH: 5.0 / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX 600 / Manufacturer: Bruker / Model: AMX 600 / Field strength: 600.13 MHz

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameDeveloperClassification
PRESTOMORIKAMI,NAKAI,KIDERA,SAITO,NAKAMURArefinement
EMBOSSstructure solution
RefinementMethod: SIMULATED ANNEALING IN 4D / Software ordinal: 1
NMR ensembleConformer selection criteria: 0.1 ANGSTROM MAXIMUM DISTANCE VIOLATION
Conformers calculated total number: 120 / Conformers submitted total number: 1

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