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- EMDB-31117: TFIID lobe C subcomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-31117
TitleTFIID lobe C subcomplex
Map data
SampleTFIID lobe C subcomplex
  • (Transcription initiation factor TFIID subunit ...) x 5
  • (nucleic-acidNucleic acid) x 2
Function / homology
Function and homology information


spermine transport / negative regulation of MHC class I biosynthetic process / TFIIH-class transcription factor complex binding / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / negative regulation of protein autoubiquitination / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / regulation of cell cycle G1/S phase transition ...spermine transport / negative regulation of MHC class I biosynthetic process / TFIIH-class transcription factor complex binding / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / negative regulation of protein autoubiquitination / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / regulation of cell cycle G1/S phase transition / SLIK (SAGA-like) complex / RNA polymerase I general transcription initiation factor activity / transcription regulator inhibitor activity / SAGA complex / RNA polymerase II-specific DNA-binding transcription factor binding / inner cell mass cell proliferation / maintenance of protein location in nucleus / positive regulation of androgen receptor activity / transcription factor catabolic process / negative regulation of histone acetylation / transcription initiation from RNA polymerase I promoter / RNA polymerase II preinitiation complex assembly / thyroid hormone receptor binding / vitamin D receptor binding / midbrain development / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / regulation of fat cell differentiation / RNA polymerase II general transcription initiation factor activity / snRNA transcription by RNA polymerase II / cellular response to ATP / transcription factor TFIID complex / ubiquitin conjugating enzyme activity / RNA polymerase II transcribes snRNA genes / positive regulation of transcription initiation from RNA polymerase II promoter / MLL1 complex / negative regulation of cell cycle / P-TEFb complex binding / RNA Polymerase II Pre-transcription Events / negative regulation of ubiquitin-dependent protein catabolic process / RNA polymerase II core promoter sequence-specific DNA binding / histone acetyltransferase binding / intracellular estrogen receptor signaling pathway / histone acetylation / histone acetyltransferase activity / histone acetyltransferase / aryl hydrocarbon receptor binding / positive regulation of intrinsic apoptotic signaling pathway / TBP-class protein binding / nuclear receptor binding => GO:0016922 / DNA-templated transcription, initiation / lysine-acetylated histone binding / response to organic cyclic compound / cellular response to UV / transcription by RNA polymerase II / negative regulation of protein kinase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of DNA-binding transcription factor activity / transcription regulator complex / p53 binding / peptidyl-threonine phosphorylation / protein polyubiquitination / G2/M transition of mitotic cell cycle / kinase activity / ubiquitin-dependent protein catabolic process / transcription initiation from RNA polymerase II promoter / sequence-specific DNA binding / protein stabilization / positive regulation of protein binding / Regulation of TP53 Activity through Phosphorylation / transcription coactivator activity / regulation of signal transduction by p53 class mediator / transcription cis-regulatory region binding / cell cycle / non-specific serine/threonine protein kinase / cell differentiation / peptidyl-serine phosphorylation / protein kinase activity / protein heterodimerization activity / negative regulation of gene expression / protein autophosphorylation / negative regulation of cell population proliferation / positive regulation of apoptotic process / chromatin / transcription factor binding / protein serine/threonine kinase activity / cellular response to DNA damage stimulus / negative regulation of transcription, DNA-templated / protein threonine kinase activity / protein serine kinase activity / apoptotic process / chromatin binding / protein phosphorylation / regulation of transcription by RNA polymerase II / viral process
Similarity search - Function
TAFII55 protein, conserved region / TAFII55 protein conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 2 / Transcription factor TFIID complex subunit 8 C-term / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID, subunit 8, C-terminal / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated ...TAFII55 protein, conserved region / TAFII55 protein conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 2 / Transcription factor TFIID complex subunit 8 C-term / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID, subunit 8, C-terminal / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated / Bromodomain associated domain / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 6 / TAF6 C-terminal HEAT repeat domain / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding / TAF6, C-terminal HEAT repeat domain / Zinc knuckle / Zinc knuckle / Protein of unknown function (DUF3591) / Transcription initiation factor TFIID subunit 1, domain of unknown function / Transcription initiation factor TFIID subunit 1 / Aminopeptidase N-like , N-terminal / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / Histone-fold / Bromodomain signature. / Bromodomain, conserved site / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Armadillo-type fold
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 1 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsChen X / Wu Z / Li J / Zhao D / Xu Y
CitationJournal: Science / Year: 2021
Title: Structural insights into preinitiation complex assembly on core promoters.
Authors: Xizi Chen / Yilun Qi / Zihan Wu / Xinxin Wang / Jiabei Li / Dan Zhao / Haifeng Hou / Yan Li / Zishuo Yu / Weida Liu / Mo Wang / Yulei Ren / Ze Li / Huirong Yang / Yanhui Xu /
Abstract: Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the ...Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the structures of human TFIID-based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA-TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)-activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters.
History
DepositionMar 24, 2021-
Header (metadata) releaseMay 12, 2021-
Map releaseMay 12, 2021-
UpdateMay 12, 2021-
Current statusMay 12, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.222
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.222
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7egh
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_31117.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 540.16 Å
1.06 Å/pix.
x 512 pix.
= 540.16 Å
1.06 Å/pix.
x 512 pix.
= 540.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density
Contour LevelBy AUTHOR: 0.222 / Movie #1: 0.222
Minimum - Maximum-3.1059234 - 5.395505
Average (Standard dev.)0.0013952557 (±0.045913033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 540.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0551.0551.055
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z540.160540.160540.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-3.1065.3960.001

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Supplemental data

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Sample components

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Entire TFIID lobe C subcomplex

EntireName: TFIID lobe C subcomplex / Number of components: 8

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Component #1: protein, TFIID lobe C subcomplex

ProteinName: TFIID lobe C subcomplex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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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: 212.956172 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: 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: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Transcription initiation factor TFIID subunit 6

ProteinName: Transcription initiation factor TFIID subunit 6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 72.749297 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: 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: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, Transcription initiation factor TFIID subunit 8

ProteinName: Transcription initiation factor TFIID subunit 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.304359 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: nucleic-acid, DNA (45-MER)

nucleic acidName: DNA (45-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (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) ...Sequence:
(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)
MassTheoretical: 22.317238 kDa
SourceSpecies: Homo sapiens (human)

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Component #8: nucleic-acid, DNA (45-MER)

nucleic acidName: DNA (45-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(DC)(DA)(DT)(DG)(DG)(DT)(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) ...Sequence:
(DA)(DT)(DC)(DC)(DA)(DT)(DG)(DG)(DT)(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)(DT) (DC)(DG)(DA)(DT)
MassTheoretical: 28.814336 kDa
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.9
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 121285
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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