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- PDB-1erj: CRYSTAL STRUCTURE OF THE C-TERMINAL WD40 DOMAIN OF TUP1 -

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Basic information

Entry
Database: PDB / ID: 1erj
TitleCRYSTAL STRUCTURE OF THE C-TERMINAL WD40 DOMAIN OF TUP1
ComponentsTRANSCRIPTIONAL REPRESSOR TUP1
KeywordsTRANSCRIPTION INHIBITOR / beta-propeller
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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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. ...Transcriptional repressor Tup1, N-terminal / Tup N-terminal / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Mainly Beta
Similarity search - Domain/homology
General transcriptional corepressor TUP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsSprague, E.R. / Redd, M.J. / Johnson, A.D. / Wolberger, C.
CitationJournal: EMBO J. / Year: 2000
Title: Structure of the C-terminal domain of Tup1, a corepressor of transcription in yeast.
Authors: Sprague, E.R. / Redd, M.J. / Johnson, A.D. / Wolberger, C.
History
DepositionApr 6, 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 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5May 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: TRANSCRIPTIONAL REPRESSOR TUP1
B: TRANSCRIPTIONAL REPRESSOR TUP1
C: TRANSCRIPTIONAL REPRESSOR TUP1


Theoretical massNumber of molelcules
Total (without water)129,9243
Polymers129,9243
Non-polymers00
Water4,774265
1
A: TRANSCRIPTIONAL REPRESSOR TUP1


Theoretical massNumber of molelcules
Total (without water)43,3081
Polymers43,3081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRANSCRIPTIONAL REPRESSOR TUP1


Theoretical massNumber of molelcules
Total (without water)43,3081
Polymers43,3081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TRANSCRIPTIONAL REPRESSOR TUP1


Theoretical massNumber of molelcules
Total (without water)43,3081
Polymers43,3081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.280, 119.280, 77.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein TRANSCRIPTIONAL REPRESSOR TUP1


Mass: 43308.137 Da / Num. of mol.: 3
Fragment: C-TERMINAL WD40 DOMAIN (RESIDUES 389 TO 431 DELETED)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P16649
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 6000, Bis-Tris Propane, NaCl, DTT, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150-100 mMbis-tris-propane1reservoir
250 mM1reservoirNaCl
323-26 %(w/v)PEG60001reservoir
42 mMdithiothreitol1reservoiror 1 mM BMS

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 30, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 53866 / Num. obs: 53856 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.308 / Num. unique all: 53788 / % possible all: 95.9
Reflection shell
*PLUS
% possible obs: 95.9 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: mlf target in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2721 -RANDOM
Rwork0.228 ---
all-54440 --
obs-53788 98.8 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7979 0 0 265 8244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.62

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