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

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Basic information

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 / homologyFATC domain / PIK-related kinase / Ub-specific processing proteases / FATC domain profile. / FAT domain profile. / FAT domain / Phosphatidylinositol 3- and 4-kinase / Transcription-associated protein 1 / Phosphatidylinositol 3-/4-kinase, catalytic domain / PIK-related kinase, FAT ...FATC domain / PIK-related kinase / Ub-specific processing proteases / FATC domain profile. / FAT domain profile. / FAT domain / Phosphatidylinositol 3- and 4-kinase / Transcription-associated protein 1 / Phosphatidylinositol 3-/4-kinase, catalytic domain / PIK-related kinase, FAT / Armadillo-type fold / Protein kinase-like domain superfamily / SLIK (SAGA-like) complex / SAGA complex / NuA4 histone acetyltransferase complex / histone acetylation / kinase activity / DNA repair / positive regulation of transcription by RNA polymerase II / transcription, DNA-templated / nucleus / Transcription-associated protein 1
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsDiaz-Santin, L.M. / Lukoyanova, N. / Aciyan, E. / Cheung, A.C.M.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 24, 2017 / Release: Aug 9, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 9, 2017Structure modelrepositoryInitial release
1.1Aug 16, 2017Structure modelDatabase referencescitation / citation_author_citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Aug 30, 2017Structure modelAuthor supporting evidence / Data collectionem_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization
1.3Jan 31, 2018Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Deposited unit
T: Transcription-associated protein 1

Theoretical massNumber of molelcules
Total (without water)436,5271

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)159900


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

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

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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 ChlorideNaCl1
30.0005 MDTTC4H10O2S21
40.0015 MMagnesium ChlorideMgCl21
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 kelvins
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.

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / Specimen holder 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)


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
4CTFFIND4.0.17CTF correction
7Coot0.8.6model fitting
9PHENIX1.11.1-2575model refinement
10RELION2.0initial Euler assignment
11RELION2.0final Euler assignment
13RELION2.03D reconstruction
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 182285 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL
Refine LS restraints
Refine 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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