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- EMDB-9298: Human TFIID BC core -

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Basic information

Entry
Database: EMDB / ID: 9298
TitleHuman TFIID BC core
Map dataprimary map
SampleGeneral transcription factor IID
  • (Transcription initiation factor TFIID subunit ...) x 9
  • poly(UNK)
Function / homologyTranscription initiation factor TFIID component TAF4 / Transcription initiation factor TFIID subunit 8 / Transcription initiation factor TFIID component TAF4 family / TAFH/NHR1 / Transcription initiation factor TFIID subunit 12 domain / Transcription initiation factor TFIID subunit A / Transcription initiation factor TFIID 23-30kDa subunit / TATA box binding protein associated factor (TAF) / Transcription initiation factor TAFII31 / Transcription initiation factor IID, 31kD subunit ...Transcription initiation factor TFIID component TAF4 / Transcription initiation factor TFIID subunit 8 / Transcription initiation factor TFIID component TAF4 family / TAFH/NHR1 / Transcription initiation factor TFIID subunit 12 domain / Transcription initiation factor TFIID subunit A / Transcription initiation factor TFIID 23-30kDa subunit / TATA box binding protein associated factor (TAF) / Transcription initiation factor TAFII31 / Transcription initiation factor IID, 31kD subunit / WD40 repeat / Histone-fold / TAF6, C-terminal HEAT repeat domain / WD domain, G-beta repeat / Transcription initiation factor TFIID subunit 2 / Bromodomain associated / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 5 / TFIID subunit TAF5, NTD2 domain superfamily / TAFH/NHR1 domain superfamily / WD40-repeat-containing domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Transcription factor TFIID, subunit 8, C-terminal / WD40-repeat-containing domain / Armadillo-type fold / WD40/YVTN repeat-like-containing domain superfamily / Transcription initiation factor TFIID, 23-30kDa subunit / WD40 associated region in TFIID subunit, NTD2 domain / NHR1 homology to TAF / Transcription of the HIV genome / RNA Polymerase II Transcription Initiation And Promoter Clearance / TFIID subunit TAF5, NTD2 domain / LIS1 homology motif / Bromodomain associated domain / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / RNA polymerase II transcribes snRNA genes / TAF6 C-terminal HEAT repeat domain / RNA Polymerase II Pre-transcription Events / Ub-specific processing proteases / HATs acetylate histones / Regulation of TP53 Activity through Phosphorylation / Trp-Asp (WD) repeats circular profile. / RNA Polymerase II HIV Promoter Escape / Transcription factor TFIID complex subunit 8 C-term / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / TATA box binding protein associated factor (TAF) / HIV Transcription Initiation / TAFH/NHR1 domain profile. / LIS1 homology (LisH) motif profile. / pre-snoRNP complex / STAGA complex / transcription factor TFTC complex / inner cell mass cell proliferation / SLIK (SAGA-like) complex / PCAF complex / regulation of DNA binding / maintenance of protein location in nucleus / SAGA complex / positive regulation of response to cytokine stimulus / histone deubiquitination / hepatocyte differentiation / regulation of fat cell differentiation / C2H2 zinc finger domain binding / box C/D snoRNP assembly / RNA polymerase II preinitiation complex assembly / snRNA transcription by RNA polymerase II / RNA polymerase binding / MLL1 complex / transcription factor TFIID complex / positive regulation of transcription initiation from RNA polymerase II promoter / cellular protein-containing complex assembly / TFIID-class transcription factor complex binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of cell cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / response to interleukin-1 / regulation of DNA-binding transcription factor activity / histone acetylation / RNA polymerase II activating transcription factor binding / DNA-templated transcription, initiation / activating transcription factor binding / ovarian follicle development / positive regulation of intrinsic apoptotic signaling pathway / thiol-dependent ubiquitinyl hydrolase activity / aryl hydrocarbon receptor binding / histone H3 acetylation / TBP-class protein binding / multicellular organism growth / G1/S transition of mitotic cell cycle / estrogen receptor binding / actin cytoskeleton / response to organic cyclic compound / p53 binding / chromatin organization / transcription regulatory region DNA binding
Function and homology information
SourceHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / 4.5 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: 6mzc

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
  • Download
  • 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-6mzc
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9298.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:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.18295214 - 0.30254063
Average (Standard dev.)0.00033880837 (0.005484348)
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-0.1830.3030.000

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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: 11

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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 2

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

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Component #3: 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 #4: 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 #5: 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 #6: 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 #7: protein, Transcription initiation factor TFIID subunit 8

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

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Component #8: 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 #9: 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 #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, poly(UNK)

ProteinName: poly(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
Support filmTreated with PEI
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: 266328
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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