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- PDB-3vp8: Crystal structure of the N-terminal domain of the yeast general c... -

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Basic information

Entry
Database: PDB / ID: 3vp8
TitleCrystal structure of the N-terminal domain of the yeast general corepressor Tup1p
ComponentsGeneral transcriptional corepressor TUP1
KeywordsTRANSCRIPTION / Four helix bundle
Function / homology
Function and homology information


carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / mediator complex binding / hyperosmotic response / phosphatidylinositol-3,5-bisphosphate binding / transcription repressor complex / histone deacetylase binding / transcription corepressor activity / histone binding / negative regulation of DNA-templated transcription / DNA damage response ...carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / mediator complex binding / hyperosmotic response / phosphatidylinositol-3,5-bisphosphate binding / transcription repressor complex / histone deacetylase binding / transcription corepressor activity / histone binding / negative regulation of DNA-templated transcription / DNA damage response / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Transcriptional repressor Tup1, N-terminal / Tup N-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat ...Transcriptional repressor Tup1, N-terminal / Tup N-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
General transcriptional corepressor TUP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsMatsumura, H. / Kusaka, N. / Nakamura, T. / Tanaka, N. / Sagegami, K. / Uegaki, K. / Inoue, T. / Mukai, Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of the N-terminal domain of the yeast general corepressor Tup1p and its functional implications
Authors: Matsumura, H. / Kusaka, N. / Nakamura, T. / Tanaka, N. / Sagegami, K. / Uegaki, K. / Inoue, T. / Mukai, Y.
History
DepositionFeb 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 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

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Assembly

Deposited unit
A: General transcriptional corepressor TUP1
B: General transcriptional corepressor TUP1
C: General transcriptional corepressor TUP1
D: General transcriptional corepressor TUP1


Theoretical massNumber of molelcules
Total (without water)44,1704
Polymers44,1704
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12690 Å2
ΔGint-101 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.170, 43.582, 70.525
Angle α, β, γ (deg.)90.00, 96.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
General transcriptional corepressor TUP1 / Flocculation suppressor protein / Glucose repression regulatory protein TUP1 / Repressor AER2


Mass: 11042.381 Da / Num. of mol.: 4 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: TUP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P16649
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: 10%(v/v) 2-propanol, 0.1M phosphate-citrate, 0.2M Li2SO4, pH 4.2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 28, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→34.6 Å / Num. all: 25047 / Num. obs: 25047 / % possible obs: 92.9 % / Observed criterion σ(F): 4.8 / Observed criterion σ(I): 4.8
Reflection shellResolution: 1.9→1.93 Å / % possible all: 92.6

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Processing

Software
NameVersionClassification
SHELXSphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.91→34.585 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7258 / SU ML: 0.22 / σ(F): 0 / Phase error: 33.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2984 1257 5.03 %RANDOM
Rwork0.2442 ---
obs0.2471 24979 92.15 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.361 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso max: 70.33 Å2 / Biso mean: 30.6573 Å2 / Biso min: 10.68 Å2
Baniso -1Baniso -2Baniso -3
1--9.9528 Å2-0 Å26.2637 Å2
2--3.8087 Å2-0 Å2
3---6.1441 Å2
Refinement stepCycle: LAST / Resolution: 1.91→34.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2623 0 0 212 2835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072651
X-RAY DIFFRACTIONf_angle_d0.8523554
X-RAY DIFFRACTIONf_chiral_restr0.056386
X-RAY DIFFRACTIONf_plane_restr0.003474
X-RAY DIFFRACTIONf_dihedral_angle_d20.2691051
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9096-1.9860.421370.35052508264589
1.986-2.07640.33631400.23682797293798
2.0764-2.18590.29211630.21392813297699
2.1859-2.32280.3401930.2861763185663
2.3228-2.50210.30981660.24132822298899
2.5021-2.75380.26941380.23262849298799
2.7538-3.15210.28321320.226128652997100
3.1521-3.97030.23191070.21162443255084
3.9703-34.59040.3191810.26852862304398

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