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- EMDB-3824: Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 -

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Basic information

Entry
Database: EMDB / ID: 3824
TitleCryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1
Map data
SampleTra1 - Transcription-associated protein 1:
Transcription-associated protein 1
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
SourceSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsDiaz-Santin LM / Lukoyanova N
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 ReportPDB-ID: 5ojs

SummaryFull reportAbout validation report
DateDeposition: Jul 24, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Aug 9, 2017 / Last update: Jan 31, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5ojs
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3824.map.gz (map file in CCP4 format, 97557 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
290 pix
1.06 Å/pix.
= 307.4 Å
290 pix
1.06 Å/pix.
= 307.4 Å
290 pix
1.06 Å/pix.
= 307.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.122903876 - 0.20766993
Average (Standard dev.)0.0005694987 (0.005844923)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions290290290
Origin000
Limit289289289
Spacing290290290
CellA=B=C: 307.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z290290290
origin x/y/z0.0000.0000.000
length x/y/z307.400307.400307.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS290290290
D min/max/mean-0.1230.2080.001

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Supplemental data

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Sample components

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Entire Tra1 - Transcription-associated protein 1

EntireName: Tra1 - Transcription-associated protein 1 / Number of components: 2
MassTheoretical: 433 kDa

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Component #1: protein, Tra1 - Transcription-associated protein 1

ProteinName: Tra1 - Transcription-associated protein 1 / Recombinant expression: No
MassTheoretical: 433 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, Transcription-associated protein 1

ProteinName: Transcription-associated protein 1 / Recombinant expression: No
MassTheoretical: 436.527281 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 94 %
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
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.4 e/Å2 / Illumination mode: OTHER
LensCs: 2.7 mm / Imaging mode: OTHER / Defocus: 1500 - 3500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 182285
3D reconstructionSoftware: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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