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

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Entry
Database: PDB / ID: 5ojs
TitleCryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1
DescriptorTranscription-associated protein 1
KeywordsTRANSCRIPTION / Coactivator / PIKK / SAGA / NuA4
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
MethodElectron microscopy (3.7 Å resolution / Particle / Single particle)
AuthorsDiaz-Santin, L.M. / Lukoyanova, N. / Aciyan, E. / Cheung, A.C.M.
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 at 3.7 angstrom resolution.
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

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Assembly

Deposited unit
T: Transcription-associated protein 1


Theoretical massNumber of molelcules
Total (without water)436,5271
Polyers436,5271
Non-polymers00
Water0
#1


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

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Components

#1: Polypeptide(L)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 /
References: UniProt: P38811

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Tra1 - Transcription-associated protein 1 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.433 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Source (recombinant)Organism: Saccharomyces cerevisiae
Buffer solutionpH: 8
Buffer component
IDConc.UnitsNameFormulaBuffer ID
10.05MHepesC8H18N2O4S1
20.15MSodium ChlorideNaCl1
30.0005MDTTC4H10O2S21
40.0015MMagnesium 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 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.

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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)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDFitting ID
4CTFFIND4.0.17CTF CORRECTION1
7Coot0.8.6MODEL FITTING1
9PHENIX1.11.1-2575MODEL REFINEMENT1
10RELION2.0INITIAL EULER ASSIGNMENT1
11RELION2.0FINAL EULER ASSIGNMENT1
12RELION2.0CLASSIFICATION1
13RELION2.0RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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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