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- EMDB-9663: Saccharomyces cerevisiae SAGA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9663
TitleSaccharomyces cerevisiae SAGA complex
Map data
Sample
  • Complex: Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex
Function / homology
Function and homology information


SLIK (SAGA-like) complex / SAGA complex / NuA4 histone acetyltransferase complex / Ub-specific processing proteases / chromatin remodeling / 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 / FAT domain profile. / FATC domain profile. / FATC domain ...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 / FAT domain profile. / FATC domain profile. / FATC domain / PIK-related kinase / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Transcription-associated protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsZheng XD / Liu GC / Guan HP / Li HT
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, 2018-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 15, 2019-
UpdateMay 22, 2019-
Current statusMay 22, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9663.png

Downloads & links

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Map

FileDownload / File: emd_9663.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 360 pix.
= 504.36 Å		1.4 Å/pix.
x 360 pix.
= 504.36 Å		1.4 Å/pix.
x 360 pix.
= 504.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.401 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.04819569 - 0.11833755
Average (Standard dev.)0.0003225751 (±0.0028834597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 504.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4011.4011.401
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z504.360504.360504.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0480.1180.000

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Supplemental data

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Mask #1

Fileemd_9663_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Z-plane reversed map, for docking and comparison.

Fileemd_9663_additional.map
AnnotationZ-plane reversed map, for docking and comparison.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_9663_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_9663_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex

EntireName: Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex
Components
  • Complex: Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex

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Supramolecule #1: Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex

SupramoleculeName: Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex
type: complex / ID: 1 / Parent: 0 / Details: The multi-functional co-activator SAGA complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BYL4741 / Organelle: Nucleus / Location in cell: Nucleus
Molecular weightTheoretical: 1.8 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8.5 / Component:
ConcentrationFormula
20.0 mMHEPES
150.0 mMNaCl
/ Details: 20mM HEPES pH 8.5 150mM Nacl
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
Details: The grid was coated with a home-made thin continuous carbon film.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsSpherical aberration corrector: Cs-corrector are used
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 3-30 / Number real images: 8526 / Average exposure time: 0.25 sec. / Average electron dose: 5.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsCs-corrector was used for data collection
Particle selectionNumber selected: 1350000 / Details: GPU accelerated Gautomatch
CTF correctionSoftware - Name: Gctf (ver. 1.06) / Software - details: GPU accelerated / Details: GPU accelerated Gctf
Startup modelType of model: OTHER / Details: We generated it using cryosparc automacially.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Software - details: GPU accelerated / Number images used: 176464
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 1.6) / Software - details: GPU accelerated / Details: We generated it using cryosparc automacially.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0) / Software - details: GPU accelerated
Details: Several rounds of refinement were used to get the best results.
Final 3D classificationSoftware - Name: RELION (ver. 2.0) / Software - details: GPU accelerated
FSC plot (resolution estimation)

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