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- PDB-6aly: Solution structure of yeast Med15 ABD2 residues 277-368 -

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Basic information

Entry
Database: PDB / ID: 6aly
TitleSolution structure of yeast Med15 ABD2 residues 277-368
ComponentsMediator of RNA polymerase II transcription subunit 15
KeywordsTRANSCRIPTION / Mediator / Transcription Activation / Helical / ABD / MED15 / Gal11 / yeast
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 / mRNA cleavage and polyadenylation specificity factor complex / core mediator complex / TFIIH-class transcription factor complex binding / 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 ...TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / positive regulation of invasive growth in response to glucose limitation / mRNA cleavage and polyadenylation specificity factor complex / core mediator complex / TFIIH-class transcription factor complex binding / 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 superfamily
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
AuthorsTuttle, L.M. / Pacheco, D. / Warfield, L. / Hahn, S. / Klevit, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM075114 United States
CitationJournal: Cell Rep / Year: 2018
Title: Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex.
Authors: Tuttle, L.M. / Pacheco, D. / Warfield, L. / Luo, J. / Ranish, J. / Hahn, S. / Klevit, R.E.
History
DepositionAug 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)10,5261
Polymers10,5261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 10525.714 Da / Num. of mol.: 1 / Fragment: UNP residues 277-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
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-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
1121isotropic13D 1H-15N TOCSY
192isotropic13D HBHA(CO)NH
1142isotropic23D H(CCO)NH
1152isotropic23D C(CO)NH
1131isotropic23D 1H-15N NOESY
1112isotropic32D 1H-15N HSQC
122isotropic33D HNCO
132isotropic33D HNCA
142isotropic33D HN(CO)CA
152isotropic33D CBCA(CO)NH
162isotropic33D HN(CA)CB
172isotropic32D 1H-13C HSQC
1102isotropic23D 1H-13C NOESY aromatic
183isotropic33D 1H-13C NOESY
1163isotropic23D (H)CCH-TOCSY
1173isotropic23D (H)CCH-COSY
1184anisotropic32D 1H-15N HSQC IPAP
1191isotropic22D 1H-15N HSQC IPAP

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution120 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 0.1 mM PMSF, 5 mM DTT, 500 uM [U-15N] Med15 ABD2, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution220 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 0.1 mM PMSF, 5 mM DTT, 500 uM [U-13C; U-15N] Med15 ABD2, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution320 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 0.1 mM PMSF, 5 mM DTT, 500 uM [U-13C; U-15N] Med15 ABD2, 100% D2O13C15Nd2o_sample100% D2O
solution420 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 0.1 mM PMSF, 5 mM DTT, 10 % C12E6/Hexanol, 2.6 mM [U-15N] Med15 ABD2, 90% H2O/10% D2O15N_c12e690% H2O/10% D2ORDC sample C12E6/Hexanol
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
0.1 mMEDTAnatural abundance1
0.1 mMPMSFnatural abundance1
5 mMDTTnatural abundance1
500 uMMed15 ABD2[U-15N]1
20 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
0.1 mMEDTAnatural abundance2
0.1 mMPMSFnatural abundance2
5 mMDTTnatural abundance2
500 uMMed15 ABD2[U-13C; U-15N]2
20 mMsodium phosphatenatural abundance3
150 mMsodium chloridenatural abundance3
0.1 mMEDTAnatural abundance3
0.1 mMPMSFnatural abundance3
5 mMDTTnatural abundance3
500 uMMed15 ABD2[U-13C; U-15N]3
20 mMsodium phosphatenatural abundance4
150 mMsodium chloridenatural abundance4
0.1 mMEDTAnatural abundance4
0.1 mMPMSFnatural abundance4
5 mMDTTnatural abundance4
10 %C12E6/Hexanolnatural abundance4
2.6 mMMed15 ABD2[U-15N]4
Sample conditionsIonic strength: 150 mM / Label: pH65 / pH: 6.5 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III5001
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE IIIBrukerAVANCE III8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
TALOSCornilescu, Delaglio and Baxstructure calculation
X-PLOR NIH2.45Schwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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