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- PDB-1yrn: CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2 HOMEODOMAIN HETERODIMER ... -

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Basic information

Entry
Database: PDB / ID: 1yrn
TitleCRYSTAL STRUCTURE OF THE MATA1/MATALPHA2 HOMEODOMAIN HETERODIMER BOUND TO DNA
Components
  • DNA (5'-D(*TP*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*C P*AP*TP*CP*A)-3')
  • DNA (5'-D(*TP*AP*TP*GP*AP*TP*GP*TP*AP*AP*TP*AP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3')
  • PROTEIN (MAT A1 HOMEODOMAIN)
  • PROTEIN (MAT ALPHA2 HOMEODOMAIN)
KeywordsDNA BINDING PROTEIN/DNA / COMPLEX / DNA-BINDING PROTEIN / DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


: / regulation of mating-type specific transcription, DNA-templated / RNA polymerase II transcription repressor complex / DNA binding, bending / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II ...: / regulation of mating-type specific transcription, DNA-templated / RNA polymerase II transcription repressor complex / DNA binding, bending / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / 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 ...: / 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
DNA / DNA (> 10) / Mating-type protein A1 / Mating-type protein ALPHA2 / Mating-type protein A1 / Silenced mating-type protein ALPHA2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLi, T. / Stark, M.R. / Johnson, A.D. / Wolberger, C.
Citation
Journal: Science / Year: 1995
Title: Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA.
Authors: Li, T. / Stark, M.R. / Johnson, A.D. / Wolberger, C.
#1: Journal: Proteins / Year: 1995
Title: Crystallization and Preliminary X-Ray Diffraction Studies of an A1/alpha2/DNA Ternary Complex
Authors: Li, T. / Stark, M. / Johnson, A.D. / Wolberger, C.
History
DepositionNov 2, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*C P*AP*TP*CP*A)-3')
D: DNA (5'-D(*TP*AP*TP*GP*AP*TP*GP*TP*AP*AP*TP*AP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3')
A: PROTEIN (MAT A1 HOMEODOMAIN)
B: PROTEIN (MAT ALPHA2 HOMEODOMAIN)


Theoretical massNumber of molelcules
Total (without water)29,8174
Polymers29,8174
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.380, 132.380, 45.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: DNA chain DNA (5'-D(*TP*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*C P*AP*TP*CP*A)-3')


Mass: 6395.183 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*AP*TP*GP*AP*TP*GP*TP*AP*AP*TP*AP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3')


Mass: 6484.246 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (MAT A1 HOMEODOMAIN)


Mass: 7164.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: T7 PROMOTER / Gene: MAT A1 RESIDUE 66-126 / Plasmid: PMS/K66 / Gene (production host): MAT A1 RESIDUE 66-126 / Production host: Escherichia coli (E. coli) / References: UniProt: P01366, UniProt: P0CY10*PLUS
#4: Protein PROTEIN (MAT ALPHA2 HOMEODOMAIN)


Mass: 9773.306 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: TAC PROMOTER / Gene: MAT ALPHA2 RESIDUE 128-210 / Plasmid: PAV105 / Gene (production host): MAT ALPHA2 RESIDUE 128-210 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B2C0, UniProt: P0CY08*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.6 %
Crystal
*PLUS
Density % sol: 67.6 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMHEPES1dropprecipitant
220 mM1dropprecipitantCaCl2
35-10 mMcobaltic hexamine1dropprecipitant
4150-200 mMHEPES1reservoir
520 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 23, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 18106 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.055
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % possible obs: 94 % / Redundancy: 4 % / Num. measured all: 76841

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Processing

Software
NameClassification
X-PLORrefinement
R-AXISdata reduction
RefinementResolution: 2.5→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.298 -10 %
Rwork0.225 --
obs0.225 14624 86.6 %
Displacement parametersBiso mean: 33.65 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 855 0 58 1909
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.93
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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