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- EMDB-0249: Structure of K. phaffii TFIID -

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Open data


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Basic information

Entry
Database: EMDB / ID: 0249
TitleStructure of K. phaffii TFIID
Map datakomagataella phaffii (formerly Pichia pastoris) TFIID
SampleTranscription Factor IIDTranscription factor II D:
SourceKomagataella phaffii GS115 (fungus)
Methodsingle particle reconstruction / cryo EM / 12.13 Å resolution
AuthorsKolesnikova O / Ben-Shem A / Luo J / Ranish J / Schultz P / Papai G
CitationJournal: Nat Commun / Year: 2018
Title: Molecular structure of promoter-bound yeast TFIID.
Authors: Olga Kolesnikova / Adam Ben-Shem / Jie Luo / Jeff Ranish / Patrick Schultz / Gabor Papai
DateDeposition: Sep 20, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0249.map.gz (map file in CCP4 format, 16385 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
2.2 Å/pix.
= 352. Å
160 pix
2.2 Å/pix.
= 352. Å
160 pix
2.2 Å/pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density
Contour Level:0.028 (by author), 0.028 (movie #1):
Minimum - Maximum-0.06075021 - 0.058848996
Average (Standard dev.)-0.00024534267 (0.0064801024)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin0.00.00.0
Limit159.0159.0159.0
Spacing160160160
CellA=B=C: 352.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z352.000352.000352.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0610.059-0.000

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Supplemental data

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Sample components

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Entire Transcription Factor IID

EntireName: Transcription Factor IID / Number of components: 1

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Component #1: protein, Transcription Factor IID

ProteinName: Transcription Factor IIDTranscription factor II D / Recombinant expression: No
MassTheoretical: 900 kDa
SourceSpecies: Komagataella phaffii GS115 (fungus)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.4 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 95 %

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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: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000.0 X (nominal) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3800.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 155620
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 12.13 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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