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- PDB-1mbf: MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 1 -

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Basic information

Entry
Database: PDB / ID: 1mbf
TitleMOUSE C-MYB DNA-BINDING DOMAIN REPEAT 1
ComponentsMYB PROTO-ONCOGENE PROTEIN
KeywordsDNA BINDING PROTEIN / PROTOONCOGENE PRODUCT
Function / homology
Function and homology information


positive regulation of testosterone secretion / skeletal muscle cell proliferation / myeloid cell development / positive regulation of hepatic stellate cell proliferation / negative regulation of hematopoietic progenitor cell differentiation / positive regulation of hepatic stellate cell activation / positive regulation of transforming growth factor beta production / T-helper 2 cell differentiation / homeostasis of number of cells / cellular response to leukemia inhibitory factor ...positive regulation of testosterone secretion / skeletal muscle cell proliferation / myeloid cell development / positive regulation of hepatic stellate cell proliferation / negative regulation of hematopoietic progenitor cell differentiation / positive regulation of hepatic stellate cell activation / positive regulation of transforming growth factor beta production / T-helper 2 cell differentiation / homeostasis of number of cells / cellular response to leukemia inhibitory factor / embryonic digestive tract development / myeloid cell differentiation / spleen development / stem cell division / positive regulation of glial cell proliferation / cellular response to interleukin-6 / thymus development / WD40-repeat domain binding / positive regulation of collagen biosynthetic process / response to ischemia / cellular response to retinoic acid / B cell differentiation / negative regulation of megakaryocyte differentiation / in utero embryonic development / positive regulation of smooth muscle cell proliferation / erythrocyte differentiation / RNA polymerase II transcription regulator complex / G1/S transition of mitotic cell cycle / positive regulation of miRNA transcription / cellular response to hydrogen peroxide / calcium ion transport / positive regulation of neuron apoptotic process / regulation of gene expression / mitotic cell cycle / DNA-binding transcription activator activity, RNA polymerase II-specific / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / DNA-templated transcription / 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 / Homeodomain-like / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...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 / Homeodomain-like / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / 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
AuthorsOgata, K. / Morikawa, S. / Nakamura, H. / Hojo, H. / Yoshimura, S. / Zhang, R. / Aimoto, S. / Ametani, Y. / Hirata, Z. / Sarai, A. ...Ogata, K. / Morikawa, S. / Nakamura, H. / Hojo, H. / Yoshimura, S. / Zhang, R. / Aimoto, S. / Ametani, Y. / Hirata, Z. / Sarai, A. / Ishii, S. / Nishimura, Y.
Citation
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. / Ishii, S. / Nishimura, Y.
#1: 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.
#2: 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
DepositionMay 19, 1995Processing site: BNL
Revision 1.0Jul 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 29, 2012Group: Database references
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYB PROTO-ONCOGENE PROTEIN


Theoretical massNumber of molelcules
Total (without water)6,3171
Polymers6,3171
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)50 / -
Representative

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Components

#1: Protein MYB PROTO-ONCOGENE PROTEIN


Mass: 6317.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GENE C-MYB, NMR, 50 STRUCTURES; ENGINEERED / Source: (natural) Mus musculus (house mouse) / References: UniProt: P06876
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditions
Conditions-IDpHTemperature (K)
16.8290 K
26.8300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameDeveloperClassification
EMBOSSNAKAI,KIDERA,NAKAMURArefinement
PRESTOMORIKAMI,NAKAI,KIDERA,SAITO,NAKAMURArefinement
RefinementSoftware ordinal: 1
Details: A TOTAL OF 50 STRUCTURES WERE CALCULATED. THE COORDINATES OF THE RESTRAINED MINIMIZED AVERAGED STRUCTURE WERE OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL STRUCTURES, AND THEN BY ...Details: A TOTAL OF 50 STRUCTURES WERE CALCULATED. THE COORDINATES OF THE RESTRAINED MINIMIZED AVERAGED STRUCTURE WERE OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL STRUCTURES, AND THEN BY SUBJECTING THE RESULTING COORDINATES TO THE RESTRAINED ENERGY MINIMIZATION BY PRESTO.
NMR ensembleConformers submitted total number: 50

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