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- EMDB-9302: Human TFIID Lobe A canonical -

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Basic information

Entry
Database: EMDB / ID: 9302
TitleHuman TFIID Lobe A canonical
Map dataprimary map
SampleGeneral transcription factor IID
  • (Transcription initiation factor TFIID subunit ...) x 10
  • TATA-box-binding protein
  • poly(UNK)
Function / homologyHistone-fold / Zinc finger, FYVE/PHD-type / TATA-box binding protein, eukaryotic / WD40-repeat-containing domain superfamily / Bromodomain-like superfamily / TAFII-230 TBP-binding domain superfamily / TAFH/NHR1 domain superfamily / TFIID subunit TAF5, NTD2 domain superfamily / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 ...Histone-fold / Zinc finger, FYVE/PHD-type / TATA-box binding protein, eukaryotic / WD40-repeat-containing domain superfamily / Bromodomain-like superfamily / TAFII-230 TBP-binding domain superfamily / TAFH/NHR1 domain superfamily / 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 TFIID subunit 3 / Transcription factor TFIID (or TATA-binding protein, TBP) / Bromodomain / Transcription initiation factor TFIID subunit 1, domain of unknown function / PHD-finger / Transcription initiation factor IID, 18kD subunit / Transcription initiation factor IID, 31kD subunit / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID subunit A / WD40 associated region in TFIID subunit, NTD2 domain / hTAFII28-like protein conserved region / Transcription initiation factor TFIID component TAF4 family / Bromodomain associated / NHR1 homology to TAF / TAF6 C-terminal HEAT repeat domain / TATA-box binding protein, conserved site / G-protein beta WD-40 repeat / Protein of unknown function (DUF3591) / Zinc finger, PHD-type / TAFII-230 TBP-binding / Transcription initiation factor TFIID component TAF4 / TFIID subunit TAF5, NTD2 domain / TAFII28-like protein / LIS1 homology motif / Bromodomain associated domain / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID, 23-30kDa subunit / TAFH/NHR1 / Transcription initiation factor TFIID subunit 12 domain / Transcription initiation factor IID, subunit 13 / Transcription initiation factor TAFII31 / WD40 repeat / Zinc finger, PHD-finger / Bromodomain / TATA-box binding protein / Transcription initiation factor TFIID subunit 1, animal / TAF6, C-terminal HEAT repeat domain / TBP domain superfamily / Zinc finger, RING/FYVE/PHD-type / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / WD40-repeat-containing domain / Bromodomain, conserved site / WD40 repeat, conserved site / Zinc finger, PHD-type, conserved site / TATA box-binding protein binding / WD domain, G-beta repeat / Transcription factor TFIID repeat signature. / RNA Polymerase II Promoter Escape / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Ub-specific processing proteases / RNA Polymerase II Pre-transcription Events / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / HATs acetylate histones / 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 / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Estrogen-dependent gene expression / SIRT1 negatively regulates rRNA expression / RNA Polymerase I Chain Elongation / Transcription of the HIV genome / HIV Transcription Initiation / Bromodomain signature. / Trp-Asp (WD) repeats signature. / Zinc finger PHD-type signature. / RNA Polymerase II HIV Promoter Escape / Bromodomain profile. / Zinc finger PHD-type profile. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / LIS1 homology (LisH) motif profile. / TAFH/NHR1 domain profile. / negative regulation of protein autoubiquitination / regulation of transcription initiation from RNA polymerase II promoter / pre-snoRNP complex / regulation of cell cycle G1/S phase transition / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage / STAGA complex
Function and homology information
SourceHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / 9.8 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: 6mzd

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 with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6mzd
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9302.png

Downloads & links

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Map

Fileemd_9302.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 size
XYZ
EMDB info.0.1320.1320.132
CCP4 map header1.321.321.32
EM Navigator Movie #11.321.321.32
Density

Histogram

Histogram (log scale)
Contour Level:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.12629227 - 0.3521133
Average (Standard dev.)-0.0003763245 (0.009759218)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin0.00.00.0
Limit287.0287.0287.0
Spacing288288288
CellA=B=C: 38.016 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-0.1260.352-0.000

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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: 13

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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

ProteinName: Transcription initiation factor TFIID subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 213.050125 kDa
SourceSpecies: Human (human)

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

ProteinName: Transcription initiation factor TFIID subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 103.76932 kDa
SourceSpecies: Human (human)

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

ProteinName: Transcription initiation factor TFIID subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 110.221883 kDa
SourceSpecies: Human (human)

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

ProteinName: Transcription initiation factor TFIID subunit 5 / 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 9

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

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Component #8: 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 #9: protein, Transcription initiation factor TFIID subunit 11

ProteinName: Transcription initiation factor TFIID subunit 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.340094 kDa
SourceSpecies: Human (human)

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Component #10: 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 #11: protein, Transcription initiation factor TFIID subunit 13

ProteinName: Transcription initiation factor TFIID subunit 13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.307068 kDa
SourceSpecies: Human (human)

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Component #12: 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 #13: protein, poly(UNK)

ProteinName: poly(UNK) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.188084 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 / Number of projections: 107900
3D reconstructionResolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

6mzd

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