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- PDB-1k1v: Solution Structure of the DNA-Binding Domain of MafG -

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Basic information

Entry
Database: PDB / ID: 1k1v
TitleSolution Structure of the DNA-Binding Domain of MafG
ComponentsMafG
KeywordsDNA BINDING PROTEIN / Maf / transcription factor / DNA-binding domain
Function / homology
Function and homology information


Factors involved in megakaryocyte development and platelet production / regulation of epidermal cell differentiation / regulation of cellular pH / adult behavior / RNA polymerase II transcription regulator complex / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific ...Factors involved in megakaryocyte development and platelet production / regulation of epidermal cell differentiation / regulation of cellular pH / adult behavior / RNA polymerase II transcription regulator complex / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus
Similarity search - Function
Transcription Factor Skn-1; Chain P / Transcription factor, Skn-1-like, DNA-binding domain / Transcription factor Maf family / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain ...Transcription Factor Skn-1; Chain P / Transcription factor, Skn-1-like, DNA-binding domain / Transcription factor Maf family / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor MafG
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsKusunoki, H. / Motohashi, H. / Katsuoka, F. / Morohashi, A. / Yamamoto, M. / Tanaka, T.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Solution structure of the DNA-binding domain of MafG.
Authors: Kusunoki, H. / Motohashi, H. / Katsuoka, F. / Morohashi, A. / Yamamoto, M. / Tanaka, T.
History
DepositionSep 25, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 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: MafG


Theoretical massNumber of molelcules
Total (without water)4,9631
Polymers4,9631
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)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide MafG / Transcription factor MafG


Mass: 4962.735 Da / Num. of mol.: 1 / Fragment: Residues 24-64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O54790

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
141HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy on 13C/15N or 15N labeled MafG(1-76).

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Sample preparation

DetailsContents: 1.5-2.0mM MafG(1-76); 20mM Sodium phosphate, 10mM Dithiothreitol-d10; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY INOVAVarianUNITY INOVA5001
Bruker AVANCE DRXBrukerAVANCE DRX8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brunger, A.T.structure solution
X-PLOR3.851Brunger, A.T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 843 restraints: 817 NOE-derived distance restraints and 26 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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