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- PDB-1f43: SOLUTION STRUCTURE OF THE MATA1 HOMEODOMAIN -

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Basic information

Entry
Database: PDB / ID: 1f43
TitleSOLUTION STRUCTURE OF THE MATA1 HOMEODOMAIN
ComponentsMATING-TYPE PROTEIN A-1
KeywordsTRANSCRIPTION / Homeodomain / helix-turn-helix
Function / homology
Function and homology information


regulation of mating-type specific transcription, DNA-templated / transcription corepressor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA binding / nucleus
Similarity search - Function
Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mating-type protein A1 / Mating-type protein A1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsAnderson, J.S. / Forman, M. / Modleski, S. / Dahlquist, F.W. / Baxter, S.M.
CitationJournal: Biochemistry / Year: 2000
Title: Cooperative ordering in homeodomain-DNA recognition: solution structure and dynamics of the MATa1 homeodomain.
Authors: Anderson, J.S. / Forman, M.D. / Modleski, S. / Dahlquist, F.W. / Baxter, S.M.
History
DepositionJun 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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: MATING-TYPE PROTEIN A-1


Theoretical massNumber of molelcules
Total (without water)7,1641
Polymers7,1641
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 / 100target function
RepresentativeModel #17closest to the average

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Components

#1: Protein MATING-TYPE PROTEIN A-1


Mass: 7164.493 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN, C-TERMINAL DOMAIN (66-126)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PCW/AL66-126 / Production host: Escherichia coli (E. coli) / References: UniProt: P01366, UniProt: P0CY10*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
122HNHA
131HNCA-J
1432D NOESY
153DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM MATa1(66-126) U-15N,13C 25 mM deuterated acetate, pH 4.5, 100 mM KCl, 0.01% NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
21.5 mM MATa1 (66-126) U-15N 25 mM deuterated acetate, pH 4.5, 100 mM KCl, 0.01% NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
31.5 mM MATa1 (66-126) 25 mM deuterated acetate, pH 4.5, 100 mM KCl, 0.01% NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM KCl 4.5ambient 298 K
2100 mM KCl 4.5ambient 298 K
3100 mM KCl 4.5ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.3Bruker Instrumentscollection
Felix970Molecular Simulations, Inc.data analysis
Felix970Molecular Simulations, Inc.processing
X-PLOR3.851A. Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structure is based on a total of 1178 NOE-derived distance constraints, 38 dihedral angle constraints, and 42 hydrogen bond restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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