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- EMDB-3804: Cryo-EM structure of the yeast chromatin modifying complex SAGA -

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Basic information

Entry
Database: EMDB / ID: EMD-3804
TitleCryo-EM structure of the yeast chromatin modifying complex SAGA
Map data
Sample
  • Complex: Spt-Ada-Gcn5-acetyltransferase complex (SAGA)
    • Protein or peptide: Cryo-EM structure of yeast SAGA complex
Biological speciesKomagataella pastoris (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.7 Å
AuthorsSharov G / Voltz K / Durand A / Kolesnikova O / Dejaegere A / Papai G / Myasnikov AG / Ben-Shem A / Schultz P
CitationJournal: Nat Commun / Year: 2017
Title: Structure of the transcription activator target Tra1 within the chromatin modifying complex SAGA.
Authors: Grigory Sharov / Karine Voltz / Alexandre Durand / Olga Kolesnikova / Gabor Papai / Alexander G Myasnikov / Annick Dejaegere / Adam Ben Shem / Patrick Schultz /
Abstract: The transcription co-activator complex SAGA is recruited to gene promoters by sequence-specific transcriptional activators and by chromatin modifications to promote pre-initiation complex formation. ...The transcription co-activator complex SAGA is recruited to gene promoters by sequence-specific transcriptional activators and by chromatin modifications to promote pre-initiation complex formation. The yeast Tra1 subunit is the major target of acidic activators such as Gal4, VP16, or Gcn4 but little is known about its structural organization. The 430 kDa Tra1 subunit and its human homolog the transformation/transcription domain-associated protein TRRAP are members of the phosphatidyl 3-kinase-related kinase (PIKK) family. Here, we present the cryo-EM structure of the entire SAGA complex where the major target of activator binding, the 430 kDa Tra1 protein, is resolved with an average resolution of 5.7 Å. The high content of alpha-helices in Tra1 enabled tracing of the majority of its main chain. Our results highlight the integration of Tra1 within the major epigenetic regulator SAGA.
History
DepositionJul 13, 2017-
Header (metadata) releaseJul 26, 2017-
Map releaseNov 29, 2017-
UpdateNov 29, 2017-
Current statusNov 29, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00289
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.00289
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3804.png

Downloads & links

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Map

FileDownload / File: emd_3804.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.00289 / Movie #1: 0.00289
Minimum - Maximum-0.013926455 - 0.020810243
Average (Standard dev.)0.000013579981 (±0.00067877065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 563.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z563.200563.200563.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0140.0210.000

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Supplemental data

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Sample components

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Entire : Spt-Ada-Gcn5-acetyltransferase complex (SAGA)

EntireName: Spt-Ada-Gcn5-acetyltransferase complex (SAGA)
Components
  • Complex: Spt-Ada-Gcn5-acetyltransferase complex (SAGA)
    • Protein or peptide: Cryo-EM structure of yeast SAGA complex

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Supramolecule #1: Spt-Ada-Gcn5-acetyltransferase complex (SAGA)

SupramoleculeName: Spt-Ada-Gcn5-acetyltransferase complex (SAGA) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 1.8 MDa

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Macromolecule #1: Cryo-EM structure of yeast SAGA complex

MacromoleculeName: Cryo-EM structure of yeast SAGA complex / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella pastoris (fungus)
SequenceString:
()

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.018 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 1 second before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.4 µm / Calibrated defocus min: 1.4 µm / Calibrated magnification: 127272 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.001 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 59000
Specialist opticsSpherical aberration corrector: Microscope has a Cs corrector
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 80.0 K
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 2-8 / Number grids imaged: 4 / Number real images: 8505 / Average exposure time: 1.0 sec. / Average electron dose: 60.0 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.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 264901
CTF correctionSoftware:
Namedetails
Gctf (ver. 0.50)CTF estimation
CTFFIND (ver. 4.0.15)CTF estimation

Details: Full CTF correction in Relion
Startup modelType of model: RANDOM CONICAL TILT
Details: RCT model from previous study: DOI: 10.1016/j.molcel.2004.06.005
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Merit function: Maximum likelihood (ML
Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 11.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 105916
FSC plot (resolution estimation)

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