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- PDB-2k0n: Solution Structure of Yeast Gal11p kix domain -

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Basic information

Entry
Database: PDB / ID: 2k0n
TitleSolution Structure of Yeast Gal11p kix domain
ComponentsMediator of RNA polymerase II transcription subunit 15
KeywordsTRANSCRIPTION / Protein / Activator / Nucleus / Phosphoprotein / Transcription regulation
Function / homology
Function and homology information


TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / positive regulation of invasive growth in response to glucose limitation / TFIIH-class transcription factor complex binding / core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II-specific DNA-binding transcription factor binding ...TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / positive regulation of invasive growth in response to glucose limitation / TFIIH-class transcription factor complex binding / core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Mediator complex, subunit Med15, fungi / Gal11, coactivator domain / Mediator complex subunit 15, KIX domain / Mediator complex subunit 15 / KIX domain / Gal11 activator-binding domain (ABD1) / Coactivator CBP, KIX domain / Coactivator CBP, KIX domain superfamily / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 15
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsArthanari, H. / Frueh, D.P. / Wagner, G.K. / Naar, A.M.
CitationJournal: Nature / Year: 2008
Title: A nuclear receptor-like pathway regulating multidrug resistance in fungi.
Authors: Thakur, J.K. / Arthanari, H. / Yang, F. / Pan, S.J. / Fan, X. / Breger, J. / Frueh, D.P. / Gulshan, K. / Li, D.K. / Mylonakis, E. / Struhl, K. / Moye-Rowley, W.S. / Cormack, B.P. / Wagner, G. / Naar, A.M.
History
DepositionFeb 4, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mediator of RNA polymerase II transcription subunit 15


Theoretical massNumber of molelcules
Total (without water)9,4091
Polymers9,4091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mediator of RNA polymerase II transcription subunit 15 / Mediator complex subunit 15 / Transcription regulatory protein GAL11 / Basal expression activator ...Mediator complex subunit 15 / Transcription regulatory protein GAL11 / Basal expression activator protein 1 / Autonomous replication regulatory protein 3 / Defective silencing suppressor protein 4 / Ty insertion suppressor protein 13


Mass: 9408.607 Da / Num. of mol.: 1 / Fragment: kix domain (UNP residues 6-90)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GAL11, ABE1, MED15, RAR3, SDS4, SPT13 / Plasmid: pet24-b / Production host: Escherichia coli (E. coli) / References: UniProt: P19659

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HNCO
1813D C(CO)NH
1913D 1H-15N TOCSY
11013D H(CCO)NH
11113D 1H-15N NOESY
NMR detailsText: The structure was determined using NOE constrains

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Sample preparation

DetailsContents: 700 uM [U-99% 13C; U-99% 15N] Gal11p, 10 mM sodium phosphate, 2 mM potassium phosphate, 137 mM sodium chloride, 2.7 mM potassium chloride, 1 mM EDTA, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
700 uMGal11p[U-99% 13C; U-99% 15N]1
10 mMsodium phosphate1
2 mMpotassium phosphate1
137 mMsodium chloride1
2.7 mMpotassium chloride1
1 mMEDTA1
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient atm / Temperature: 288.3 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE9002
Varian INOVAVarianINOVA6003
Bruker AMXBrukerAMX6004

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Processing

NMR softwareName: CYANA / Version: v2.1 / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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