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- PDB-6ig9: Tra1 subunit from Saccharomyces cerevisiae SAGA complex -

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Basic information

Entry
Database: PDB / ID: 6ig9
TitleTra1 subunit from Saccharomyces cerevisiae SAGA complex
ComponentsTranscription-associated protein 1
KeywordsTRANSCRIPTION / Epigenetics / Acetyltransferase / Co-activator
Function / homology
Function and homology information


TTT Hsp90 cochaperone complex / SLIK (SAGA-like) complex / SAGA complex / DNA repair-dependent chromatin remodeling / NuA4 histone acetyltransferase complex / Ub-specific processing proteases / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...TTT Hsp90 cochaperone complex / SLIK (SAGA-like) complex / SAGA complex / DNA repair-dependent chromatin remodeling / NuA4 histone acetyltransferase complex / Ub-specific processing proteases / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / : / PIK-related kinase, FAT / FAT domain / FATC domain / PIK-related kinase / FAT domain profile. ...Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / : / PIK-related kinase, FAT / FAT domain / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
SAGA complex/NuA4 acetyltransferase complex subunit TRA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsZheng, X.D. / Liu, G.C. / Guan, H.P. / Li, H.T.
CitationJournal: Cell Discov / Year: 2019
Title: Architecture of SAGA complex.
Authors: Gaochao Liu / Xiangdong Zheng / Haipeng Guan / Yong Cao / Hongyuan Qu / Junqing Kang / Xiangle Ren / Jianlin Lei / Meng-Qiu Dong / Xueming Li / Haitao Li /
History
DepositionSep 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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  • EMDB-9664
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Structure viewerMolecule:
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Assembly

Deposited unit
T: Transcription-associated protein 1


Theoretical massNumber of molelcules
Total (without water)433,6771
Polymers433,6771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area199030 Å2

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Components

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


Mass: 433677.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BYL4741 / 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 / ScTra1 / Type: COMPLEX
Details: One of the major part from SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex
Entity ID: all / Source: NATURAL
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Cellular location: nucleus / Organelle: Nucleus
Buffer solutionpH: 8.5 / Details: 20mM HEPES pH 8.5 150mM Nacl
Buffer component
IDConc.FormulaBuffer-ID
120 mMHEPES1
2150 mMNaCl1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: We extracted it from the overall SAGA complex structure.
Specimen supportDetails: The grid was coated with a home-made thin continuous carbon film.
Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281 K
Details: Blot for 4 seconds and wait for 30 seconds before plunging

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 3000 nm / Cs: 0.1 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 5.6 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8526
EM imaging opticsSpherical aberration corrector: With a Cs-corrector
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 32 / Used frames/image: 3-30

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Processing

SoftwareName: PHENIX / Version: dev_3290: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1Gautomatch0.56particle selectionGPU accelerated
4Gctf1.06CTF correctionGPU accelerated
7PHENIX1.13model fitting
9PHENIX1.13model refinement
10cryoSPARC1.6initial Euler assignmentGPU accelerated
11RELION2final Euler assignmentGPU accelerated
12RELION2classificationGPU accelerated
13RELION23D reconstructionGPU accelerated
CTF correctionDetails: GPU accelerated / Type: NONE
Particle selectionNum. of particles selected: 1350000 / Details: GPU accelerated
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176464 / Algorithm: FOURIER SPACE / Details: GPU accelerated / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 5OJS

5ojs


Accession code: 5OJS / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00717220
ELECTRON MICROSCOPYf_angle_d1.0224103
ELECTRON MICROSCOPYf_dihedral_angle_d5.63810366
ELECTRON MICROSCOPYf_chiral_restr0.0513304
ELECTRON MICROSCOPYf_plane_restr0.0093481

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