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- PDB-5ojs: Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 -

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Basic information

Entry
Database: PDB / ID: 5ojs
TitleCryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1
ComponentsTranscription-associated protein 1
KeywordsTRANSCRIPTION / Coactivator / PIKK / SAGA / NuA4
Function / homology
Function and homology information


ASTRA complex / SLIK (SAGA-like) complex / SAGA complex / NuA4 histone acetyltransferase complex / histone acetylation / transcription coregulator activity / DNA repair / protein phosphorylation / regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / nucleus
FAT domain / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Transcription-associated protein 1 / Armadillo-type fold / PIK-related kinase / Protein kinase-like domain superfamily / FATC domain / PIK-related kinase, FAT
Transcription-associated protein 1
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDiaz-Santin, L.M. / Lukoyanova, N. / Aciyan, E. / Cheung, A.C.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust102535/Z/13/Z United Kingdom
Royal SocietyRG140138 United Kingdom
CitationJournal: Elife / Year: 2017
Title: Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 at 3.7 angstrom resolution.
Authors: Luis Miguel Díaz-Santín / Natasha Lukoyanova / Emir Aciyan / Alan Cm Cheung /
Abstract: Coactivator complexes SAGA and NuA4 stimulate transcription by post-translationally modifying chromatin. Both complexes contain the Tra1 subunit, a highly conserved 3744-residue protein from the ...Coactivator complexes SAGA and NuA4 stimulate transcription by post-translationally modifying chromatin. Both complexes contain the Tra1 subunit, a highly conserved 3744-residue protein from the Phosphoinositide 3-Kinase-related kinase (PIKK) family and a direct target for multiple sequence-specific activators. We present the Cryo-EM structure of Tra1 to 3.7 Å resolution, revealing an extensive network of alpha-helical solenoids organized into a diamond ring conformation and is strikingly reminiscent of DNA-PKcs, suggesting a direct role for Tra1 in DNA repair. The structure was fitted into an existing SAGA EM reconstruction and reveals limited contact surfaces to Tra1, hence it does not act as a molecular scaffold within SAGA. Mutations that affect activator targeting are distributed across the Tra1 structure, but also cluster within the N-terminal Finger region, indicating the presence of an activator interaction site. The structure of Tra1 is a key milestone in deciphering the mechanism of multiple coactivator complexes.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.3Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Assembly

Deposited unit
T: Transcription-associated protein 1


Theoretical massNumber of molelcules
Total (without water)436,5271
Polymers436,5271
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area159900 Å2
MethodPISA

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Components

#1: Protein Transcription-associated protein 1 / p400 kDa component of SAGA


Mass: 436527.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TRA1, YHR099W / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38811

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tra1 - Transcription-associated protein 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.433 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
10.05 MHepesC8H18N2O4S1
20.15 MSodium ChlorideNaClSodium chloride1
30.0005 MDTTC4H10O2S21
40.0015 MMagnesium ChlorideMgCl21
51
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Agar Scientific
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 94 % / Chamber temperature: 277 K
Details: Two subsequent applications of protein were required to achieve the desired particle density on grids. Each application was followed by 20 sec waiting time, with a short 0.5 sec blotting ...Details: Two subsequent applications of protein were required to achieve the desired particle density on grids. Each application was followed by 20 sec waiting time, with a short 0.5 sec blotting after first application and 5 sec blotting after the second.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4.0.17CTF correction
7Coot0.8.6model fitting
9PHENIX1.11.1-2575model refinement
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182285 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00729026
ELECTRON MICROSCOPYf_angle_d1.40939323
ELECTRON MICROSCOPYf_dihedral_angle_d10.04417644
ELECTRON MICROSCOPYf_chiral_restr0.0714501
ELECTRON MICROSCOPYf_plane_restr0.0094969

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