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- EMDB-31116: TFIID lobe B subcomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-31116
TitleTFIID lobe B subcomplex
Map data
SampleTFIID lobe B subcomplex
  • (Transcription initiation factor TFIID subunit ...) x 7
Function / homology
Function and homology information


pre-snoRNP complex / DNA-templated transcription open complex formation / STAGA complex / transcription factor TFTC complex / PCAF complex / SLIK (SAGA-like) complex / regulation of DNA binding / SAGA complex / positive regulation of response to cytokine stimulus / inner cell mass cell proliferation ...pre-snoRNP complex / DNA-templated transcription open complex formation / STAGA complex / transcription factor TFTC complex / PCAF complex / SLIK (SAGA-like) complex / regulation of DNA binding / SAGA complex / positive regulation of response to cytokine stimulus / inner cell mass cell proliferation / maintenance of protein location in nucleus / histone deubiquitination / hepatocyte differentiation / box C/D snoRNP assembly / C2H2 zinc finger domain binding / RNA polymerase binding / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / regulation of fat cell differentiation / RNA polymerase II general transcription initiation factor activity / snRNA transcription by RNA polymerase II / transcription factor TFIID complex / RNA polymerase II transcribes snRNA genes / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of transcription initiation from RNA polymerase II promoter / cellular protein-containing complex assembly / MLL1 complex / negative regulation of cell cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA Polymerase II Pre-transcription Events / ovarian follicle development / histone acetylation / DNA-binding transcription factor binding => GO:0140297 / histone H3 acetylation / aryl hydrocarbon receptor binding / positive regulation of intrinsic apoptotic signaling pathway / TBP-class protein binding / response to interleukin-1 / promoter-specific chromatin binding / DNA-templated transcription, initiation / G1/S transition of mitotic cell cycle / transcription by RNA polymerase II / multicellular organism growth / estrogen receptor binding / actin cytoskeleton / p53 binding / HATs acetylate histones / positive regulation of DNA-binding transcription factor activity / ATPase binding / transcription initiation from RNA polymerase II promoter / protein stabilization / Regulation of TP53 Activity through Phosphorylation / regulation of gene expression / transcription coactivator activity / regulation of signal transduction by p53 class mediator / transcription cis-regulatory region binding / Ub-specific processing proteases / protein deubiquitination / cell differentiation / protein heterodimerization activity / negative regulation of cell population proliferation / positive regulation of apoptotic process / chromatin / transcription factor binding / cellular response to DNA damage stimulus / apoptotic process / regulation of transcription, DNA-templated / viral process / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4 / TAFH/NHR1 domain superfamily / Bromodomain associated / NHR1 homology to TAF / Bromodomain transcription factors and PHD domain containing proteins / TAFH/NHR1 domain profile. ...Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4 / TAFH/NHR1 domain superfamily / Bromodomain associated / NHR1 homology to TAF / Bromodomain transcription factors and PHD domain containing proteins / TAFH/NHR1 domain profile. / TAF homology / Transcription initiation factor IID, 31kD subunit / Bromodomain associated domain / Transcription initiation factor TFIID subunit A / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / TAFH/NHR1 / WD40 associated region in TFIID subunit, NTD2 domain / TFIID subunit TAF5, NTD2 domain superfamily / Transcription initiation factor TAFII31 / TATA box binding protein associated factor (TAF) / TFIID subunit TAF5, NTD2 domain / TAF6 C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 12 domain / Transcription initiation factor TFIID subunit 6 / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / LIS1 homology (LisH) motif profile. / LIS1 homology motif / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / Histone-fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Armadillo-type fold / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 4 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 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 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 19, 2021-
Current statusMay 19, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7egg
  • Surface level: 0.5
  • 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_31116.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.4 Å
0.82 Å/pix.
x 320 pix.
= 262.4 Å
0.82 Å/pix.
x 320 pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.37 / Movie #1: 0.5
Minimum - Maximum-1.9962667 - 3.5641859
Average (Standard dev.)-8.295925e-05 (±0.09974613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z262.400262.400262.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.9963.564-0.000

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Supplemental data

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Sample components

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Entire TFIID lobe B subcomplex

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

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Component #1: protein, TFIID lobe B subcomplex

ProteinName: TFIID lobe B 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 4

ProteinName: Transcription initiation factor TFIID subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 110.221883 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Transcription initiation factor TFIID subunit 5

ProteinName: Transcription initiation factor TFIID subunit 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 86.932109 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: 1 / 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 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 #6: protein, Transcription initiation factor TFIID subunit 9

ProteinName: Transcription initiation factor TFIID subunit 9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.006838 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: 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: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: 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: Homo sapiens (human)
Source (engineered)Expression System: 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
VitrificationCryogen 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: 63 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: 84427
3D reconstructionResolution: 2.77 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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