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- PDB-6hqa: Molecular structure of promoter-bound yeast TFIID -

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Basic information

Entry
Database: PDB / ID: 6hqa
TitleMolecular structure of promoter-bound yeast TFIID
Components
  • (Histone-fold) x 2
  • Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
  • Subunit (60 kDa) of TFIID and SAGA complexes
  • Subunit (61/68 kDa) of TFIID and SAGA complexes
  • Subunit (90 kDa) of TFIID and SAGA complexes
  • TFIID subunit (48 kDa)Transcription factor II D
  • Taf2
  • Taf8
KeywordsTRANSCRIPTION / Complex / Transcription initiation
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 / transcription factor TFIID complex / protein-containing complex scaffold activity / RNA polymerase II preinitiation complex assembly / histone acetylation / RNA polymerase II activating transcription factor binding / DNA-templated transcription, initiation / regulation of transcription by RNA polymerase II / 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
Specimen sourceKomagataella phaffii GS115 (fungus)
Komagataella phaffii (fungus)
MethodELECTRON MICROSCOPY / single 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 Report
SummaryFull reportAbout validation report
DateDeposition: Sep 24, 2018 / Release: Nov 21, 2018

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-0251
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Taf2
B: Subunit (90 kDa) of TFIID and SAGA complexes
C: Subunit (90 kDa) of TFIID and SAGA complexes
D: Subunit (60 kDa) of TFIID and SAGA complexes
E: Subunit (60 kDa) of TFIID and SAGA complexes
F: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
G: Taf8
I: Histone-fold
H: Histone-fold
K: Subunit (61/68 kDa) of TFIID and SAGA complexes
J: TFIID subunit (48 kDa)


Theoretical massNumber of molelcules
Total (without water)634,42911
Polyers634,42911
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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Protein/peptide , 9 types, 11 molecules ABCDEFGIHKJ

#1: Protein/peptide Taf2


Mass: 199179.078 Da / Num. of mol.: 1 / Source: (natural) Komagataella phaffii GS115 (fungus)
#2: Protein/peptide Subunit (90 kDa) of TFIID and SAGA complexes


Mass: 80933.008 Da / Num. of mol.: 2
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R4L4
#3: Protein/peptide Subunit (60 kDa) of TFIID and SAGA complexes


Mass: 54888.445 Da / Num. of mol.: 2
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4QW33
#4: Protein/peptide Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation


Mass: 17303.576 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4QZS5
#5: Protein/peptide Taf8


Mass: 6400.881 Da / Num. of mol.: 1 / Source: (natural) Komagataella phaffii GS115 (fungus)
#6: Protein/peptide Histone-fold


Mass: 5464.728 Da / Num. of mol.: 1 / Source: (natural) Komagataella phaffii GS115 (fungus)
#7: Protein/peptide Histone-fold


Mass: 5805.147 Da / Num. of mol.: 1 / Source: (natural) Komagataella phaffii GS115 (fungus)
#8: Protein/peptide Subunit (61/68 kDa) of TFIID and SAGA complexes


Mass: 66690.133 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R150
#9: Protein/peptide TFIID subunit (48 kDa) / Transcription factor II D


Mass: 61942.883 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R420

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Transcription Factor IIDTranscription factor II D / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9 / Source: NATURAL
Molecular weightValue: 0.9 MDa / Experimental value: NO
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
Buffer solutionpH: 8
SpecimenConc.: 0.4 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 / Calibrated magnification: 45454 / Nominal defocus max: 3800 / Nominal defocus min: 1200 / Calibrated defocus min: 800 / Calibrated defocus max: 4900 / Cs: 0.01 / C2 aperture diameter: 70 / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 / Electron dose: 52.8 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 / Phase plate: None / Sph aberration corrector: Equipped with Cs corrector
Image scansSampling size: 5 / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 3-40

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Processing

EM software
IDNameCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 295734
SymmetryPoint symmetry: C1
3D reconstructionResolution: 7.1 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 180823 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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