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- PDB-5oej: Structure of Tra1 subunit within the chromatin modifying complex SAGA -

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Database: PDB / ID: 5oej
TitleStructure of Tra1 subunit within the chromatin modifying complex SAGA
ComponentsTra1 subunit within the chromatin modifying complex SAGA
KeywordsTRANSCRIPTION / yeast / Tra1 / SAGA / activator target
Specimen sourceKomagataella pastoris / fungus
MethodElectron microscopy (5.7 Å resolution / Particle / Single particle)
AuthorsSharov, G. / Voltz, K. / Durand, A. / Kolesnikova, O. / Papai, G. / Myasnikov, A.G. / Dejaegere, A. / Ben-Shem, A. / Schultz, P.
CitationNat Commun, 2017, 8, 1556-1556

Nat Commun, 2017, 8, 1556-1556 Yorodumi Papers
Structure of the transcription activator target Tra1 within the chromatin modifying complex SAGA.
Grigory Sharov / Karine Voltz / Alexandre Durand / Olga Kolesnikova / Gabor Papai / Alexander G Myasnikov / Annick Dejaegere / Adam Ben Shem / Patrick Schultz

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 7, 2017 / Release: Aug 2, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Aug 9, 2017Structure modelDatabase references / Structure summaryaudit_author / citation_author_audit_author.name / _citation_author.name
1.2Sep 20, 2017Structure modelDatabase referencespdbx_database_related_pdbx_database_related.db_id
1.3Nov 29, 2017Structure modelDatabase referencescitation / citation_author_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

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Deposited unit
B: Tra1 subunit within the chromatin modifying complex SAGA

Theoretical massNumber of molelcules
Total (without water)438,0551

TypeNameSymmetry operationNumber
identity operation1_5551


#1: Protein/peptide Tra1 subunit within the chromatin modifying complex SAGA

Mass: 438055.344 Da / Num. of mol.: 1 / Source: (natural) Komagataella pastoris / fungus / References: UniProt: F2QQ15

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Tra1 subunit of SAGA complex / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 0.4 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Komagataella pastoris
Buffer solutionpH: 8
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 kelvins / Details: Blot for 1 second before plunging

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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 / Calibrated magnification: 127272 / Nominal defocus max: 3400 nm / Nominal defocus min: 1400 nm / Calibrated defocus min: 1400 nm / Calibrated defocus max: 3400 nm / Cs: 0.001 mm / C2 aperture diameter: 100 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 kelvins / Temperature (min): 70 kelvins
Image recordingAverage exposure time: 1 sec. / Electron dose: 60 e/Å2
Details: Images were collected in movie-mode at 17 frames per second, frame 1 was not acquired. Every two frames were joined together, producing 8 frames per second.
Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 4 / Number of real images: 8505
EM imaging opticsSph aberration corrector: Microscope has a Cs corrector
Image scansSampling size: 14 microns / Dimension width: 4096 / Dimension height: 4096 / Movie frames/image: 8 / Used frames/image: 2-8


EM software
1Gautomatch0.53PARTICLE SELECTIONWas used for auto-picking
4Gctf0.50CTF CORRECTIONCTF estimation
8UCSF Chimera1.9MODEL FITTINGrigid-body with "fit in map" tool
9Situs2.6MODEL FITTINGrigid-body with "colores" tool
15Coot0.8.7MODEL REFINEMENTreal-space refinement
16PHENIX1.11MODEL REFINEMENTgeometry minimization
CTF correctionDetails: Full CTF correction in Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 264901
SymmetryPoint symmetry: C1
3D reconstructionResolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 105916 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingDetails: Secondary structure restraints were applied in Phenix.
Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model buildingPDB-ID: 4JSN
Pdb chain ID: B / Pdb chain residue range: 1385-2549
Least-squares processHighest resolution: 5.7 Å

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