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- PDB-2lpb: Structure of the complex of the central activation domain of Gcn4... -

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Basic information

Entry
Database: PDB / ID: 2lpb
TitleStructure of the complex of the central activation domain of Gcn4 bound to the mediator co-activator domain 1 of Gal11/med15
Components
  • General control protein GCN4
  • Mediator of RNA polymerase II transcription subunit 15
KeywordsTRANSCRIPTION / Mediator / Activator / Co-Activator / Nucleus / Phosphoprotein / Transcription regulation / amino acid biosynthesis / DNA-binding
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 / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation ...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 / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / RNA polymerase II preinitiation complex assembly / cellular response to amino acid starvation / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
Helix Hairpins - #2920 / 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) / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. ...Helix Hairpins - #2920 / 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) / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Coactivator CBP, KIX domain superfamily / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
General control transcription factor GCN4 / Mediator of RNA polymerase II transcription subunit 15
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsBrzovic, P.S. / Heikaus, C.C. / Kisselev, L. / Vernon, R. / Herbig, E. / Pacheco, D. / Warfield, L. / Littlefield, P. / Baker, D. / Klevit, R.E. / Hahn, S.
CitationJournal: Mol.Cell / Year: 2011
Title: The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex.
Authors: Brzovic, P.S. / Heikaus, C.C. / Kisselev, L. / Vernon, R. / Herbig, E. / Pacheco, D. / Warfield, L. / Littlefield, P. / Baker, D. / Klevit, R.E. / Hahn, S.
History
DepositionFeb 7, 2012Deposition site: BMRB / Processing site: RCSB
SupersessionFeb 22, 2012ID: 2KO4
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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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
B: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)13,4732
Polymers13,4732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)13 / 13structures with the lowest energy
RepresentativeModel #1

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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: 9515.047 Da / Num. of mol.: 1 / Fragment: UNP residues 158-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ABE1, GAL11, MED15, RAR3, SDS4, SPT13, YOL051W / Production host: Escherichia coli (E. coli) / References: UniProt: P19659
#2: Protein/peptide General control protein GCN4 / Amino acid biosynthesis regulatory protein


Mass: 3958.076 Da / Num. of mol.: 1
Fragment: Transcriptional activation region, residues 101-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: AAS3, ARG9, GCN4, YEL009C / Production host: Escherichia coli (E. coli) / References: UniProt: P03069

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1333D CBCA(CO)NH
1453D CBCA(CO)NH
1533D HNCA
1653D HNCA
1733D HNCO
1853D HNCO
1933D HN(CA)CB
11053D HN(CA)CB
11133D 1H-15N NOESY
11253D 1H-15N NOESY
11343D 1H-13C NOESY aliphatic
11453D 1H-13C NOESY aliphatic
11543D 1H-13C NOESY aromatic
11653D 1H-13C NOESY aromatic
11733D C(CO)NH
11853D C(CO)NH
11933D H(CCO)NH
12053D H(CCO)NH
12132D 1H-13C HSQC aliphatic
12252D 1H-13C HSQC aliphatic
12332D 1H-13C HSQC aromatic
12452D 1H-13C HSQC aromatic
NMR detailsText: The authors state that the structures are arranged by energy, preceeding from lowest to highest, but there is no single representative structure. Binding of Gcn4 residues 101-134 to Gal11 ...Text: The authors state that the structures are arranged by energy, preceeding from lowest to highest, but there is no single representative structure. Binding of Gcn4 residues 101-134 to Gal11 residues 158-238 is best represented by the entire ensemble as Gcn4 binds in multiple orientations.

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Sample preparation

Details
Solution-IDContentsSolvent system
11-1.2 mM [U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
22-2.4 mM Gal11, 1-1.2 mM [U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
31-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
41-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT, 100% D2O100% D2O
52-2.4 mM Gal11, 1-1.2 mM [U-13C; U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMGal11-1[U-15N]1-1.21
mMGcn4-22-2.41
20 mMSodum phosphate-31
150 mMSodum chloride-41
1 mMPMSF-51
5 mMDTT-61
mMGal11-72-2.42
mMGcn4-8[U-15N]1-1.22
20 mMSodum phosphate-92
150 mMSodum chloride-102
1 mMPMSF-112
5 mMDTT-122
mMGal11-13[U-13C; U-15N]1-1.23
mMGcn4-142-2.43
20 mMSodum phosphate-153
150 mMSodum chloride-163
1 mMPMSF-173
5 mMDTT-183
mMGal11-19[U-13C; U-15N]1-1.24
mMGcn4-202-2.44
20 mMSodum phosphate-214
150 mMSodum chloride-224
1 mMPMSF-234
5 mMDTT-244
mMGal11-252-2.45
mMGcn4-26[U-13C; U-15N]1-1.25
20 mMSodum phosphate-275
150 mMSodum chloride-285
1 mMPMSF-295
5 mMDTT-305
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA6003
Bruker DMXBrukerDMX5004

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
HADDOCK2.1Alexandre Bonvinstructure solution
VNMRVariancollection
TopSpinBruker Biospincollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 13 / Conformers submitted total number: 13

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