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- PDB-1akh: MAT A1/ALPHA2/DNA TERNARY COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1akh
TitleMAT A1/ALPHA2/DNA TERNARY COMPLEX
Components
  • DNA (5'-D(*TP*AP*CP*AP*TP*GP*TP*AP*AP*AP*AP*AP*TP*TP*TP*AP*C P*AP*TP*CP*A)-3')
  • DNA (5'-D(*TP*AP*TP*GP*AP*TP*GP*TP*AP*AP*AP*TP*TP*TP*TP*TP*A P*CP*AP*TP*G)-3')
  • PROTEIN (MATING-TYPE PROTEIN A-1)
  • PROTEIN (MATING-TYPE PROTEIN ALPHA-2)
KeywordsDNA BINDING PROTEIN/DNA / COMPLEX (TWO DNA-BINDING PROTEINS-DNA) / COMPLEX / DNA-BINDING PROTEIN / DNA / TRANSCRIPTION REGULATION / 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 / 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 ...: / 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 / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, T. / Jin, Y. / Vershon, A.K. / Wolberger, C.
Citation
Journal: Nucleic Acids Res. / Year: 1998
Title: Crystal structure of the MATa1/MATalpha2 homeodomain heterodimer in complex with DNA containing an A-tract.
Authors: Li, T. / Jin, Y. / Vershon, A.K. / Wolberger, C.
#1: Journal: Proteins / Year: 1995
Title: Crystallization and Preliminary X-Ray Diffraction Studies of an A1/Alpha 2/DNA Ternary Complex
Authors: Li, T. / Stark, M. / Johnson, A.D. / Wolberger, C.
#2: 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.
#3: Journal: Science / Year: 1995
Title: Erratum. Crystal Structure of the MATa1/MAT Alpha 2 Homeodomain Heterodimer Bound to DNA
Authors: Li, T. / Stark, M.R. / Johnson, A.D. / Wolberger, C.
History
DepositionMay 19, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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*AP*AP*AP*TP*TP*TP*AP*C P*AP*TP*CP*A)-3')
D: DNA (5'-D(*TP*AP*TP*GP*AP*TP*GP*TP*AP*AP*AP*TP*TP*TP*TP*TP*A P*CP*AP*TP*G)-3')
A: PROTEIN (MATING-TYPE PROTEIN A-1)
B: PROTEIN (MATING-TYPE PROTEIN ALPHA-2)


Theoretical massNumber of molelcules
Total (without water)29,8184
Polymers29,8184
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.250, 132.250, 45.250
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*AP*AP*AP*TP*TP*TP*AP*C P*AP*TP*CP*A)-3')


Mass: 6413.210 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*AP*TP*TP*TP*TP*TP*A P*CP*AP*TP*G)-3')


Mass: 6466.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (MATING-TYPE PROTEIN A-1)


Mass: 7165.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAT A1 RESIDUES 66 - 126 / Plasmid: PMS-K66 / Gene (production host): MAT A1 RESIDUES 66 - 126 / Production host: Escherichia coli (E. coli) / References: UniProt: P01366, UniProt: P0CY10*PLUS
#4: Protein PROTEIN (MATING-TYPE PROTEIN ALPHA-2)


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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100MM HEPES PH 7.0, 20MM CACL2, 5MM [CO(NH3)6]CL3., VAPOR DIFFUSION, HANGING DROP, temperature 295.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2HEPES BUFFER11
3CACL211
4COBALT HEXAMINE11
5WATER12
6HEPES BUFFER12
7CACL212
Crystal
*PLUS
Density % sol: 67.6 %
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMHEPES1drop
210 mM1dropCaCl2
32.5-5 mMcobaltic hexamine1drop
4150-200 mMHEPES1reservoir
520 mM1reservoirCaCl2
61
71

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1995
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 15656 / % possible obs: 83.6 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.054 / Rsym value: 7.4
Reflection shellResolution: 2.4→2.48 Å / % possible all: 67
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % possible obs: 83.6 % / Observed criterion σ(I): 1 / Num. measured all: 31013 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YRN

1yrn


Resolution: 2.5→6 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.302 -10 %RANDOM
Rwork0.201 ---
obs-12913 --
Displacement parametersBiso mean: 34.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 855 0 51 1907
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.87
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
LS refinement shellResolution: 2.5→2.58 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.389 1 10 %
Rwork0.324 935 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2RNA-DNA.PARMTOPH19.PEP
X-RAY DIFFRACTION3PARAM11.INTRNA-DNA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.324

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