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- EMDB-0251: Molecular structure of promoter-bound yeast TFIID -

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Basic information

Entry
Database: EMDB / ID: 0251
TitleMolecular structure of promoter-bound yeast TFIID
Map dataKomagataella phaffii TFIID
SampleTranscription Factor IIDTranscription factor II D
  • Taf2
  • Subunit (90 kDa) of TFIID and SAGA complexes
  • Subunit (60 kDa) of TFIID and SAGA complexes
  • Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
  • Taf8
  • (Histone-fold) x 2
  • Subunit (61/68 kDa) of TFIID and SAGA complexes
  • TFIID subunit (48 kDa)Transcription factor II D
Function / homologyWD40-repeat-containing domain / LIS1 homology motif / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 5 / TFIID subunit TAF5, NTD2 domain superfamily / WD40-repeat-containing domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Transcription initiation factor IID, 31kD subunit / Armadillo-type fold ...WD40-repeat-containing domain / LIS1 homology motif / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 5 / TFIID subunit TAF5, NTD2 domain superfamily / WD40-repeat-containing domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Transcription initiation factor IID, 31kD subunit / Armadillo-type fold / WD40/YVTN repeat-like-containing domain superfamily / TAF6, C-terminal HEAT repeat domain / Histone-fold / Transcription initiation factor TFIID component TAF4 / TFIID subunit TAF5, NTD2 domain / TATA box binding protein associated factor (TAF) / WD domain, G-beta repeat / Transcription initiation factor TFIID subunit 12 domain / Transcription initiation factor TAFII31 / WD40 repeat / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit A / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TFIID component TAF4 family / TAF6 C-terminal HEAT repeat domain / LisH / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / LIS1 homology (LisH) motif profile. / Transcription initiation factor TFIID subunit 6 / SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II preinitiation complex assembly / transcription factor TFIID complex / protein-containing complex scaffold activity / histone acetylation / regulation of DNA-binding transcription factor activity / RNA polymerase II activating transcription factor binding / DNA-templated transcription, initiation / chromatin binding / protein heterodimerization activity / identical protein binding / cytosol / Subunit (60 kDa) of TFIID and SAGA complexes / Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation / Subunit (61/68 kDa) of TFIID and SAGA complexes / TFIID subunit (48 kDa) / Subunit (90 kDa) of TFIID and SAGA complexes
Function and homology information
SourceKomagataella phaffii GS115 (fungus) / Yeast (fungus)
Methodsingle particle reconstruction / cryo EM / 7.1 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
Validation ReportPDB-ID: 6hqa

SummaryFull reportAbout validation report
DateDeposition: Sep 24, 2018 / Header (metadata) release: Oct 3, 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: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6hqa
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0251.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour Level:0.004 (by author), 0.004 (movie #1):
Minimum - Maximum-0.014203308 - 0.022313362
Average (Standard dev.)0.000059873146 (0.00071648543)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin0.00.00.0
Limit319.0319.0319.0
Spacing320320320
CellA=B=C: 352.0 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/z320320320
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/NS320320320
D min/max/mean-0.0140.0220.000

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Supplemental data

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Mask #1

Fileemd_0251_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Transcription Factor IID

EntireName: Transcription Factor IID / Number of components: 10

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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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Component #2: protein, Taf2

ProteinName: Taf2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 199.179078 kDa
SourceSpecies: Komagataella phaffii GS115 (fungus)

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Component #3: protein, Subunit (90 kDa) of TFIID and SAGA complexes

ProteinName: Subunit (90 kDa) of TFIID and SAGA complexes / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 80.933008 kDa
SourceSpecies: Yeast (fungus)

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Component #4: protein, Subunit (60 kDa) of TFIID and SAGA complexes

ProteinName: Subunit (60 kDa) of TFIID and SAGA complexes / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 54.888445 kDa
SourceSpecies: Yeast (fungus)

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Component #5: protein, Subunit (17 kDa) of TFIID and SAGA complexes, involved i...

ProteinName: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.303576 kDa
SourceSpecies: Yeast (fungus)

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Component #6: protein, Taf8

ProteinName: Taf8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.400881 kDa
SourceSpecies: Komagataella phaffii GS115 (fungus)

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Component #7: protein, Histone-fold

ProteinName: Histone-fold / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.464728 kDa
SourceSpecies: Komagataella phaffii GS115 (fungus)

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Component #8: protein, Histone-fold

ProteinName: Histone-fold / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.805147 kDa
SourceSpecies: Komagataella phaffii GS115 (fungus)

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Component #9: protein, Subunit (61/68 kDa) of TFIID and SAGA complexes

ProteinName: Subunit (61/68 kDa) of TFIID and SAGA complexes / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.690133 kDa
SourceSpecies: Yeast (fungus)

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Component #10: protein, TFIID subunit (48 kDa)

ProteinName: TFIID subunit (48 kDa)Transcription factor II D / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 61.942883 kDa
SourceSpecies: Yeast (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: 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: 1200.0 - 3800.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 180823
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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