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- PDB-1mnm: YEAST MATALPHA2/MCM1/DNA TERNARY TRANSCRIPTION COMPLEX CRYSTAL ST... -

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Basic information

Entry
Database: PDB / ID: 1mnm
TitleYEAST MATALPHA2/MCM1/DNA TERNARY TRANSCRIPTION COMPLEX CRYSTAL STRUCTURE
Components
  • (DNA (STE6 OPERATOR DNA)) x 2
  • PROTEIN (MAT ALPHA-2 TRANSCRIPTIONAL REPRESSOR)
  • PROTEIN (MCM1 TRANSCRIPTIONAL REGULATOR)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / TRANSCRIPTIONAL REPRESSION / DNA-BINDING PROTEIN / COMPLEX (TRANSCRIPTION-HOMEOBOX-DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


RNA polymerase II cis-regulatory region sequence-specific DNA binding, bending / positive regulation of arginine biosynthetic process / NGF-stimulated transcription / regulation of mating type switching / negative regulation of arginine catabolic process / : / regulation of mating-type specific transcription, DNA-templated / : / RNA polymerase II transcription repressor complex / arginine metabolic process ...RNA polymerase II cis-regulatory region sequence-specific DNA binding, bending / positive regulation of arginine biosynthetic process / NGF-stimulated transcription / regulation of mating type switching / negative regulation of arginine catabolic process / : / regulation of mating-type specific transcription, DNA-templated / : / RNA polymerase II transcription repressor complex / arginine metabolic process / DNA binding, bending / DNA replication origin binding / molecular sequestering activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / G2/M transition of mitotic cell cycle / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
MADS SRF-like / : / SRF-like / Transcription factor, MADS-box / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS ...MADS SRF-like / : / SRF-like / Transcription factor, MADS-box / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Mating-type protein ALPHA2 / Pheromone receptor transcription factor / Silenced mating-type protein ALPHA2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsTan, S. / Richmond, T.J.
Citation
Journal: Nature / Year: 1998
Title: Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex.
Authors: Tan, S. / Richmond, T.J.
#1: Journal: Nature / Year: 1995
Title: Structure of Serum Response Factor Core Bound to DNA
Authors: Pellegrini, L. / Tan, S. / Richmond, T.J.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1991
Title: Crystal Structure of a MAT Alpha 2 Homeodomain-Operator Complex Suggests a General Model for Homeodomain-DNA Interactions
Authors: Wolberger, C. / Vershon, A.K. / Liu, B. / Johnson, A.D. / Pabo, C.O.
History
DepositionNov 3, 1997Processing site: NDB
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2017Group: Source and taxonomy / Structure summary
Revision 1.4Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
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
E: DNA (STE6 OPERATOR DNA)
F: DNA (STE6 OPERATOR DNA)
A: PROTEIN (MCM1 TRANSCRIPTIONAL REGULATOR)
B: PROTEIN (MCM1 TRANSCRIPTIONAL REGULATOR)
C: PROTEIN (MAT ALPHA-2 TRANSCRIPTIONAL REPRESSOR)
D: PROTEIN (MAT ALPHA-2 TRANSCRIPTIONAL REPRESSOR)


Theoretical massNumber of molelcules
Total (without water)59,4476
Polymers59,4476
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.620, 72.550, 150.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (STE6 OPERATOR DNA)


Mass: 8019.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (STE6 OPERATOR DNA)


Mass: 7952.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein PROTEIN (MCM1 TRANSCRIPTIONAL REGULATOR) / PHEROMONE RECEPTOR TRANSCRIPTION FACTOR


Mass: 11422.067 Da / Num. of mol.: 2 / Fragment: RESIDUES 1 - 100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / Keywords: FRAGMENT: RESIDUES 1 - 100 / References: UniProt: P11746
#4: Protein PROTEIN (MAT ALPHA-2 TRANSCRIPTIONAL REPRESSOR) / MATING-TYPE PROTEIN ALPHA-2


Mass: 10315.832 Da / Num. of mol.: 2 / Fragment: RESIDUES 113 - 189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / Keywords: FRAGMENT: RESIDUES 113 - 189 / References: UniProt: Q6B2C0, UniProt: P0CY08*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Description: ADDITIONAL LOW RESOLUTION DATA SET COLLECTED USING ROTATING ANODE GENERATOR.
Crystal growpH: 5.5 / Details: pH 5.50
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 35613 / % possible obs: 94.6 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.8
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 1.7 / % possible all: 0.9
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 20 Å / % possible obs: 94.6 % / Num. measured all: 327727
Reflection shell
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 2.29 Å / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SRS AND PDB ENTRY 1APL

1srs

1apl


Resolution: 2.25→25 Å / Rfactor Rfree error: 0.7 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: BULK SOLVENT MODEL USED IN X-PLOR. TNT REFINEMENT PACKAGE ALSO USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1846 5 %RANDOM
Rwork0.24 ---
obs0.24 3670598 98.3 %-
Displacement parametersBiso mean: 52.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20 Å20 Å2
2---2.1 Å20 Å2
3----0.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 1060 0 53 3657
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.231.5
X-RAY DIFFRACTIONx_mcangle_it5.062
X-RAY DIFFRACTIONx_scbond_it4.592
X-RAY DIFFRACTIONx_scangle_it6.432.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 313 5.2 %
Rwork0.359 5718 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 25 Å / Num. reflection obs: 34859 / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.24 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21
X-RAY DIFFRACTIONx_mcbond_it3.231.5
X-RAY DIFFRACTIONx_scbond_it4.592
X-RAY DIFFRACTIONx_mcangle_it5.062
X-RAY DIFFRACTIONx_scangle_it6.432.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.36 / % reflection Rfree: 5.2 %

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