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- EMDB-3790: Structure of Tra1 subunit within the chromatin modifying complex SAGA -

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Basic information

Entry
Database: EMDB / ID: 3790
TitleStructure of Tra1 subunit within the chromatin modifying complex SAGA
SampleTra1 subunit of SAGA complex
SourceKomagataella pastoris / fungus
Map data
Methodsingle particle reconstruction, at 5.7 Å resolution
AuthorsSharov G / Voltz K
CitationTo Be Published

To Be Published Search PubMed
Structure of the transcription activator target Tra1 within the chromatin modifying complex SAGA
Sharov G / Voltz K / Durand A / Kolesnikova O / Papai G / Myasnikov AG / Dejaegere A / Ben-Shem A / Schultz P

Validation ReportPDB-ID: 5oej

SummaryFull reportAbout validation report
DateDeposition: Jul 7, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Aug 2, 2017 / Last update: Sep 20, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0429
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 0.0429
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5oej
  • Surface level: 0.0429
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_3790.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.1 Å/pix.
= 352. Å
320 pix
1.1 Å/pix.
= 352. Å
320 pix
1.1 Å/pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour Level:0.0429 (by author), 0.0429 (movie #1):
Minimum - Maximum-0.113799304 - 0.19173111
Average (Standard dev.)0.00015792702 (0.005900146)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 352 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z352.000352.000352.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1140.1920.000

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Supplemental data

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Sample components

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Entire Tra1 subunit of SAGA complex

EntireName: Tra1 subunit of SAGA complex / Number of components: 2
MassTheoretical: 400 kDa

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Component #1: protein, Tra1 subunit of SAGA complex

ProteinName: Tra1 subunit of SAGA complex / Recombinant expression: No
MassTheoretical: 400 kDa
SourceSpecies: Komagataella pastoris / fungus

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Component #2: protein, Tra1 subunit within the chromatin modifying complex SAGA

ProteinName: Tra1 subunit within the chromatin modifying complex SAGA
Recombinant expression: No
MassTheoretical: 438.055344 kDa
SourceSpecies: Komagataella pastoris / fungus

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Experimental details

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Sample preparation

Specimen stateparticle
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: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 127272 X (calibrated) / Cs: 0.001 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400 - 3400 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 70 - 80 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: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Details: Secondary structure restraints were applied in Phenix.
Input PDB model: 4JSN
Chain ID: 4JSN_B
Output model

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