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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: 3804
TitleCryo-EM structure of the yeast chromatin modifying complex SAGA
Map data
SampleSpt-Ada-Gcn5-acetyltransferase complex (SAGA):
Cryo-EM structure of yeast SAGA complex
SourceKomagataella pastoris (fungus)
Methodsingle particle reconstruction / cryo EM / 11.7 Å resolution
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
DateDeposition: Jul 13, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Nov 29, 2017 / Last update: Nov 29, 2017

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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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3804.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.1 Å/pix.
= 563.2 Å
512 pix
1.1 Å/pix.
= 563.2 Å
512 pix
1.1 Å/pix.
= 563.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour Level:0.00289 (by author), 0.00289 (movie #1):
Minimum - Maximum-0.013926455 - 0.020810243
Average (Standard dev.)0.000013579981 (0.00067877065)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin0.00.00.0
Limit511.0511.0511.0
Spacing512512512
CellA=B=C: 563.2 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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) / Number of components: 2

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Component #1: protein, Spt-Ada-Gcn5-acetyltransferase complex (SAGA)

ProteinName: Spt-Ada-Gcn5-acetyltransferase complex (SAGA) / Recombinant expression: No
MassTheoretical: 1.8 MDa
SourceSpecies: Komagataella pastoris (fungus)

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Component #2: protein, Cryo-EM structure of yeast SAGA complex

ProteinName: Cryo-EM structure of yeast SAGA complex / Recombinant expression: No
SourceSpecies: Komagataella pastoris (fungus)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 95 % / Details: Blot for 1 second before plunging.

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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: 6 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal), 127272.0 X (calibrated) / Cs: 0.001 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400.0 - 3400.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 70.0 - 80.0 K)
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 8505 / Sampling size: 14 microns
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.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 105916
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / CTF correction: Full CTF correction in Relion / Resolution: 11.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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