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- EMDB-9306: Human TFIID bound to promoter DNA and TFIIA -

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Entry
Database: EMDB / ID: 9306
TitleHuman TFIID bound to promoter DNA and TFIIA
Map dataPrimary map
SampleGeneral transcription factor IID
  • (Transcription initiation factor TFIID subunit ...) x 11
  • TATA-box-binding protein
  • (nucleic-acidNucleic acid) x 2
  • (Transcription initiation factor IIA subunit ...) x 2
  • Unk
Function / homologyTATA-box binding protein, eukaryotic / Transcription factor TFIID complex subunit 8 C-term / WD40-repeat-containing domain superfamily / Bromodomain associated domain / LIS1 homology motif / Transcription initiation factor TFIID component TAF4 family / TAFII55 protein, conserved region / TFIID subunit TAF5, NTD2 domain / Bromodomain associated / NHR1 homology to TAF ...TATA-box binding protein, eukaryotic / Transcription factor TFIID complex subunit 8 C-term / WD40-repeat-containing domain superfamily / Bromodomain associated domain / LIS1 homology motif / Transcription initiation factor TFIID component TAF4 family / TAFII55 protein, conserved region / TFIID subunit TAF5, NTD2 domain / Bromodomain associated / NHR1 homology to TAF / TAF6 C-terminal HEAT repeat domain / Transcription factor TFIID repeat signature. / Transcription initiation factor TFIID, 23-30kDa subunit / Transcription initiation factor TFIID component TAF4 / Histone-fold / TAFH/NHR1 domain superfamily / Transcription factor IIA, helical / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / LIS1 homology (LisH) motif profile. / TAFH/NHR1 domain profile. / HIV Transcription Initiation / TATA box binding protein associated factor (TAF) / TAFII55 protein conserved region / Transcription of the HIV genome / Transcription initiation factor TFIID subunit 7 / TATA-box binding protein / WD40 repeat / Transcription initiation factor TAFII31 / TFIID subunit TAF5, NTD2 domain superfamily / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / WD40 associated region in TFIID subunit, NTD2 domain / Transcription factor TFIID (or TATA-binding protein, TBP) / WD domain, G-beta repeat / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TFIID subunit 12 domain / Transcription initiation factor IIA, gamma subunit / TAFH/NHR1 / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID subunit A / RNA Polymerase II HIV Promoter Escape / Trp-Asp (WD) repeats signature. / HATs acetylate histones / Armadillo-type fold / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase I Transcription Termination / RNA Polymerase III Abortive And Retractive Initiation / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / Transcription factor IIA, beta-barrel / WD40/YVTN repeat-like-containing domain superfamily / WD40-repeat-containing domain / RNA Polymerase II Promoter Escape / Transcription factor TFIID, subunit 8, C-terminal / WD40 repeat, conserved site / G-protein beta WD-40 repeat / RNA Polymerase III Transcription Initiation From Type 1 Promoter / TATA-box binding protein, conserved site / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Estrogen-dependent gene expression / RNA Polymerase I Chain Elongation / Transcription initiation factor IIA, gamma subunit, N-terminal / TBP domain superfamily / SIRT1 negatively regulates rRNA expression / RNA Polymerase II Pre-transcription Events / Regulation of TP53 Activity through Phosphorylation / RNA Polymerase I Promoter Escape / B-WICH complex positively regulates rRNA expression / NoRC negatively regulates rRNA expression / RNA polymerase II transcribes snRNA genes / Ub-specific processing proteases / RNA Polymerase I Transcription Initiation / Transcription initiation factor IIA, gamma subunit, C-terminal / TAF6, C-terminal HEAT repeat domain / spermine transport / P-TEFb complex binding / regulation of transcription initiation from RNA polymerase II promoter / pre-snoRNP complex / RNA polymerase II general transcription initiation factor activity / STAGA complex / transcription factor TFTC complex / TFIIH-class transcription factor complex binding / inner cell mass cell proliferation / PCAF complex / SLIK (SAGA-like) complex / regulation of DNA binding / maintenance of protein location in nucleus / SAGA complex / transcription factor TFIIIB complex / transcription factor TFIIA complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase III preinitiation complex assembly
Function and homology information
SourceHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / 7.5 Å resolution
AuthorsPatel AB / Louder RK / Greber BJ / Grunberg S / Luo J / Fang J / Liu Y / Ranish J / Hahn S / Nogales E
CitationJournal: Science / Year: 2018
Title: Structure of human TFIID and mechanism of TBP loading onto promoter DNA.
Authors: Avinash B Patel / Robert K Louder / Basil J Greber / Sebastian Grünberg / Jie Luo / Jie Fang / Yutong Liu / Jeff Ranish / Steve Hahn / Eva Nogales
Abstract: The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and ...The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and initiating PIC assembly. We used cryo-electron microscopy (cryo-EM), chemical crosslinking-mass spectrometry (CX-MS) and biochemical reconstitution to determine the complete molecular architecture of TFIID and define the conformational landscape of TFIID in the process of TATA-box binding protein (TBP) loading onto promoter DNA. Our structural analysis revealed five structural states of TFIID in the presence of TFIIA and promoter DNA, showing that the initial binding of TFIID to the downstream promoter positions the upstream DNA and facilitates scanning of TBP for a TATA-box and the subsequent engagement of the promoter. Our findings provide a mechanistic model for the specific loading of TBP by TFIID onto the promoter.
Validation ReportPDB-ID: 6mzm

SummaryFull reportAbout validation report
DateDeposition: Nov 5, 2018 / Header (metadata) release: Nov 28, 2018 / Map release: Nov 28, 2018 / Last update: Nov 28, 2018

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Structure visualization

Movie
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6mzm
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9306.map.gz (map file in CCP4 format, 95552 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
1.32 Å/pix.
= 380.16 Å
288 pix
1.32 Å/pix.
= 380.16 Å
288 pix
1.32 Å/pix.
= 380.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.039078873 - 0.118663885
Average (Standard dev.)0.00023230643 (0.0047335494)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin0.00.00.0
Limit287.0287.0287.0
Spacing288288288
CellA=B=C: 380.16 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z380.160380.160380.160
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0390.1190.000

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Supplemental data

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Sample components

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Entire General transcription factor IID

EntireName: General transcription factor IID / Number of components: 18

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Component #1: protein, General transcription factor IID

ProteinName: General transcription factor IID / Recombinant expression: No
SourceSpecies: Homo sapiens (human) / Strain: HeLa

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Component #2: protein, Transcription initiation factor TFIID subunit 1, TAF1

ProteinName: Transcription initiation factor TFIID subunit 1, TAF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.193742 kDa
SourceSpecies: Human (human)

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Component #3: protein, Transcription initiation factor TFIID subunit 2, TAF2

ProteinName: Transcription initiation factor TFIID subunit 2, TAF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 137.159984 kDa
SourceSpecies: Human (human)

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Component #4: protein, Transcription initiation factor TFIID subunit 4, TAF4

ProteinName: Transcription initiation factor TFIID subunit 4, TAF4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.052086 kDa
SourceSpecies: Human (human)

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Component #5: protein, Transcription initiation factor TFIID subunit 5,TAF5

ProteinName: Transcription initiation factor TFIID subunit 5,TAF5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 85.785164 kDa
SourceSpecies: Human (human)

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Component #6: protein, Transcription initiation factor TFIID subunit 6

ProteinName: Transcription initiation factor TFIID subunit 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.749297 kDa
SourceSpecies: Human (human)

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Component #7: protein, Transcription initiation factor TFIID subunit 6

ProteinName: Transcription initiation factor TFIID subunit 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.365836 kDa
SourceSpecies: Human (human)

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Component #8: protein, Transcription initiation factor TFIID subunit 7

ProteinName: Transcription initiation factor TFIID subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.325117 kDa
SourceSpecies: Human (human)

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Component #9: protein, Transcription initiation factor TFIID subunit 8, TAF8

ProteinName: Transcription initiation factor TFIID subunit 8, TAF8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.975344 kDa
SourceSpecies: Human (human)

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Component #10: protein, Transcription initiation factor TFIID subunit 9, TAF9

ProteinName: Transcription initiation factor TFIID subunit 9, TAF9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.830689 kDa
SourceSpecies: Human (human)

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Component #11: protein, Transcription initiation factor TFIID subunit 10

ProteinName: Transcription initiation factor TFIID subunit 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.731248 kDa
SourceSpecies: Human (human)

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Component #12: protein, Transcription initiation factor TFIID subunit 12

ProteinName: Transcription initiation factor TFIID subunit 12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.948467 kDa
SourceSpecies: Human (human)

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Component #13: protein, TATA-box-binding protein

ProteinName: TATA-box-binding protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.729938 kDa
SourceSpecies: Human (human)

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Component #14: nucleic-acid, SCP DNA (80-MER)

Nucleic-acidName: SCP DNA (80-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DC)(DG)(DT)(DA)(DG)(DG)(DC)(DA)(DC) (DG)(DT)(DC)(DT)(DG)(DC)(DT)(DC)(DG)(DG) (DC)(DT)(DC)(DG)(DA)(DG)(DT)(DG)(DT)(DT) (DC)(DG)(DA)(DT)(DC)(DG)(DC)(DG)(DA)(DC) (DT)(DG)(DA)(DG)(DG)(DA)(DC)(DG)(DA)(DA) (DC)(DG)(DC)(DG)(DC)(DC)(DC)(DC)(DC)(DA) (DC)(DC)(DC)(DC)(DC)(DT)(DT)(DT)(DT)(DA) (DT)(DA)(DG)(DG)(DC)(DG)(DC)(DC)(DC)(DT)
MassTheoretical: 24.498586 kDa
SourceSpecies: Homo sapiens (human)

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Component #15: nucleic-acid, SCP DNA (80-MER)

Nucleic-acidName: SCP DNA (80-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DG)(DG)(DG)(DC)(DG)(DC)(DC)(DT)(DA) (DT)(DA)(DA)(DA)(DA)(DG)(DG)(DG)(DG)(DG) (DT)(DG)(DG)(DG)(DG)(DG)(DC)(DG)(DC)(DG) (DT)(DT)(DC)(DG)(DT)(DC)(DC)(DT)(DC)(DA) (DG)(DT)(DC)(DG)(DC)(DG)(DA)(DT)(DC)(DG) (DA)(DA)(DC)(DA)(DC)(DT)(DC)(DG)(DA)(DG) (DC)(DC)(DG)(DA)(DG)(DC)(DA)(DG)(DA)(DC) (DG)(DT)(DG)(DC)(DC)(DT)(DA)(DC)(DG)(DG)
MassTheoretical: 24.854842 kDa
SourceSpecies: Homo sapiens (human)

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Component #16: protein, Transcription initiation factor IIA subunit 1

ProteinName: Transcription initiation factor IIA subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.675194 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #17: protein, Transcription initiation factor IIA subunit 2

ProteinName: Transcription initiation factor IIA subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.275824 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #18: protein, Unk

ProteinName: Unk / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.272906 kDa
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: .2 mg/ml / pH: 7.9
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 % / Details: BT 4s; BF 15N.

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 25180
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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