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- PDB-1a5j: CHICKEN B-MYB DNA BINDING DOMAIN, REPEAT 2 AND REPEAT3, NMR, 32 S... -

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Basic information

Entry
Database: PDB / ID: 1a5j
TitleCHICKEN B-MYB DNA BINDING DOMAIN, REPEAT 2 AND REPEAT3, NMR, 32 STRUCTURES
ComponentsB-MYB
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / PROTOONCOGENE PRODUCT
Function / homology
Function and homology information


transcription coregulator activity / mitotic cell cycle / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / 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 / nucleus
Similarity search - Function
C-myb, C-terminal / C-myb, C-terminal / Myb-like DNA-binding domain / 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 ...C-myb, C-terminal / C-myb, C-terminal / Myb-like DNA-binding domain / 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
Myb-related protein B
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing
AuthorsMcintosh, P.B. / Carr, M.D. / Wollborn, U. / Frenkiel, T.A. / Feeney, J. / Mccormick, J.E. / Klempnauer, K.H.
Citation
Journal: Biochemistry / Year: 1998
Title: Solution structure of the B-Myb DNA-binding domain: a possible role for conformational instability of the protein in DNA binding and control of gene expression.
Authors: McIntosh, P.B. / Frenkiel, T.A. / Wollborn, U. / McCormick, J.E. / Klempnauer, K.H. / Feeney, J. / Carr, M.D.
#1: Journal: Eur.J.Biochem. / Year: 1996
Title: Structure of the B-Myb DNA-Binding Domain in Solution and Evidence for Multiple Conformations in the Region of Repeat-2 Involved in DNA Binding. Implications for Sequence-Specific DNA Binding by Myb Proteins
Authors: Carr, M.D. / Wollborn, U. / Mcintosh, P.B. / Frenkiel, T.A. / Mccormick, J.E. / Bauer, C.J. / Klempnauer, K.H. / Feeney, J.
History
DepositionFeb 16, 1998Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
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_keywords.text
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: B-MYB


Theoretical massNumber of molelcules
Total (without water)12,9591
Polymers12,9591
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 100NO DISTANCE CONSTRAINT ORVAN DER WAALS VIOLATIONS >0.5A,NO DIHEDRAL ANGLE CONSTRAINT VIOLATIONS >6 DEGREES
Representative

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Components

#1: Protein B-MYB


Mass: 12958.922 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN, REPEAT 2 AND REPEAT 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: PGEX-3X / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q03237

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
121TOCSY
131NOESY
1412D 1H/13C HMQC
1512D F2 12C-FILTERED TOCSY
1613D 1H/13C HMQC-NOESY
171(H)CCH-COSY
181(H)CCH-TOCSY
1913D 1H/15N NOESY-HSQC
1101NOESY-HMQC
1111HNHA
1121HNHB
1131HMQC-NOESY-HMQC
1141ROESY-HMQC
1151TOCSY-HMQC
11613D-1H/15N/13C CBCANH
1171CBCA(CO)NH
NMR detailsText: THE STRUCTURES WERE DETERMINED USING DOUBLE AND TRIPLE RESONANCE NMR SPECTROSCOPY ON 13C/15N AND 15N LABELED B-MYB.

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Sample preparation

Sample conditionspH: 6.0 / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY6001
Varian UNITYVarianUNITY5002

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Processing

Software
NameClassification
DYANAmodel building
DYANArefinement
NMR software
NameClassification
DYANAstructure solution
DYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: NO DISTANCE CONSTRAINT ORVAN DER WAALS VIOLATIONS >0.5A,NO DIHEDRAL ANGLE CONSTRAINT VIOLATIONS >6 DEGREES
Conformers calculated total number: 100 / Conformers submitted total number: 32

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