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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


myeloid cell development / embryonic digestive tract development / myeloid cell differentiation / stem cell division / cellular response to interleukin-6 / WD40-repeat domain binding / homeostasis of number of cells / spleen development / B cell differentiation / cellular response to leukemia inhibitory factor ...myeloid cell development / embryonic digestive tract development / myeloid cell differentiation / stem cell division / cellular response to interleukin-6 / WD40-repeat domain binding / homeostasis of number of cells / spleen development / B cell differentiation / cellular response to leukemia inhibitory factor / thymus development / G1/S transition of mitotic cell cycle / RNA polymerase II transcription regulator complex / calcium ion transport / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / 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 / 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
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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