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- EMDB-0250: Taf1 lobe of kpTFIID -

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Basic information

Database: EMDB / ID: 0250
TitleTaf1 lobe of kpTFIID
Map dataTaf1 lobe of Komagataella phaffi TFIID
SampleTranscription Factor IIDTranscription factor II D:
SourceKomagataella phaffii GS115 (fungus)
Methodsingle particle reconstruction / cryo EM / 10.7 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

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0185
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0185
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_0250.map.gz (map file in CCP4 format, 16385 KB)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Contour Level:0.0185 (by author), 0.0185 (movie #1):
Minimum - Maximum-0.01301578 - 0.048004474
Average (Standard dev.)-0.00007170189 (0.004115313)


Space Group Number1
Map Geometry
Axis orderXYZ
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
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0130.048-0.000

Supplemental data

Sample components

Entire Transcription Factor IID

EntireName: Transcription Factor IID / Number of components: 1

Component #1: protein, Transcription Factor IID

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

Experimental details

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 %

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: 52.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000.0 X (nominal), 45454.0 X (calibrated) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: 0.6 nm / Energy filter: GIF Quantum LS
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionSampling size: 5 microns

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 28491
3D reconstructionSoftware: RELION / Resolution: 10.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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