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- EMDB-31125: TFIID-based core PIC on CLAM2 promoter -

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Basic information

Entry
Database: EMDB / ID: EMD-31125
TitleTFIID-based core PIC on CLAM2 promoter
Map data
SampleTFIID-based core PIC on CLAM2 promoter
Function / homology
Function and homology information


negative regulation of MHC class I biosynthetic process / spermine transport / TFIIH-class transcription factor complex binding / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / pre-snoRNP complex / SAGA complex => GO:0000124 / RNA polymerase II core complex assembly / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex ...negative regulation of MHC class I biosynthetic process / spermine transport / TFIIH-class transcription factor complex binding / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / pre-snoRNP complex / SAGA complex => GO:0000124 / RNA polymerase II core complex assembly / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / RNA Pol II CTD phosphorylation and interaction with CE / TP53 Regulates Transcription of DNA Repair Genes / mRNA Splicing - Minor Pathway / Estrogen-dependent gene expression / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / Processing of Capped Intron-Containing Pre-mRNA / Transcriptional regulation by small RNAs / mRNA Splicing - Major Pathway / FGFR2 alternative splicing / mRNA Capping / RNA polymerase II transcribes snRNA genes / transcription factor TFTC complex / Dual incision in TC-NER / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / negative regulation of protein autoubiquitination / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / negative regulation of MHC class II biosynthetic process / SAGA complex => GO:0000124 / phosphatase activator activity / TFIIF-class transcription factor complex binding / regulation of cell cycle G1/S phase transition / SLIK (SAGA-like) complex / positive regulation of core promoter binding / regulation of DNA binding / transcription factor TFIIF complex / RNA polymerase I general transcription initiation factor activity / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / SAGA complex / transcription regulator inhibitor activity / RNA Polymerase III Transcription Initiation From Type 3 Promoter / positive regulation of response to cytokine stimulus / inner cell mass cell proliferation / RNA Polymerase III Abortive And Retractive Initiation / RNA polymerase II-specific DNA-binding transcription factor binding / maintenance of protein location in nucleus / RNA polymerase III general transcription initiation factor activity / histone deubiquitination / transcription factor TFIIA complex / hepatocyte differentiation / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of androgen receptor activity / RNA Polymerase I Transcription Termination / general transcription initiation factor activity / RNA polymerase II general transcription initiation factor binding / negative regulation of histone acetylation / box C/D snoRNP assembly / transcription factor catabolic process / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / positive regulation by host of viral transcription / RNA Pol II CTD phosphorylation and interaction with CE / C2H2 zinc finger domain binding / FGFR2 alternative splicing / male pronucleus / Formation of the HIV-1 Early Elongation Complex / Formation of the Early Elongation Complex / female pronucleus / Viral Messenger RNA Synthesis / mRNA Capping / RNA polymerase binding / positive regulation of viral transcription / thyroid hormone receptor binding / vitamin D receptor binding / transcription initiation from RNA polymerase I promoter / RNA polymerase II preinitiation complex assembly / Processing of Capped Intron-Containing Pre-mRNA / midbrain development / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / HIV Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / regulation of fat cell differentiation / termination of RNA polymerase I transcription / RNA polymerase complex / Signaling by FGFR2 IIIa TM / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / Pausing and recovery of HIV elongation / HIV elongation arrest and recovery
Similarity search - Function
TAFII28-like protein domain / hTAFII28-like protein conserved region / 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 ...TAFII28-like protein domain / hTAFII28-like protein conserved region / 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 / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor IID, 18kD subunit / Transcription initiation factor IID, subunit 13 / Transcription initiation factor TFIID component TAF4, C-terminal / Bromodomain associated / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAFH/NHR1 domain superfamily / TAF homology / Bromodomain transcription factors and PHD domain containing proteins / Transcription initiation factor IID, 31kD subunit / Bromodomain associated domain / Transcription initiation factor TFIID subunit A / Transcription initiation factor TFIID subunit 12 / TAFH/NHR1 / Transcription initiation factor TFIID subunit 5 / 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) / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 12 domain / TAF6 C-terminal HEAT repeat domain / TFIID subunit TAF5, NTD2 domain / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / TAFII-230 TBP-binding / TAFII-230 TBP-binding domain superfamily / Transcription initiation factor TFIID subunit 1, animal / TATA box-binding protein binding / 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 / TFIIF, beta subunit N-terminus / TFIIF, beta subunit, N-terminal / Transcription initiation factor IIF, beta subunit / TFIIF, beta subunit HTH domain / TFIIF beta subunit, HTH domain / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / LIS1 homology (LisH) motif profile. / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription factor IIA, beta-barrel / LIS1 homology motif / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / TFIIB zinc-binding / Zinc finger, TFIIB-type / TATA-box binding protein, eukaryotic / TATA-box binding protein / Transcription factor TFIID repeat signature. / Transcription factor TFIID (or TATA-binding protein, TBP) / TATA-box binding protein, conserved site / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb4/RPC9, core / TBP domain superfamily / Aminopeptidase N-like , N-terminal / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit RPB4/RPC9 / RNA polymerase Rpb4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like , N-terminal / Zinc finger TFIIS-type signature. / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / domain present in cyclins, TFIIB and Retinoblastoma / RNA polymerase Rpb2, domain 5 / Cyclin-like / Cyclin-like superfamily
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 3 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor IIB ...Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 3 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIA subunit 1 / General transcription factor IIF subunit 1 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 1 / TATA-box-binding protein / General transcription factor IIF subunit 2 / Transcription initiation factor TFIID subunit 4 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit E / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA_pol_L_2 domain-containing protein / DNA-directed RNA polymerase subunit beta / Uncharacterized protein / DNA-directed RNA polymerase II subunit RPB4 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsChen X / Yilun Q / Hou H / Wang X / Wu Z / Li J / 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) releaseApr 14, 2021-
Map releaseApr 14, 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: 0.44
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.44
  • 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_31125.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.28 Å/pix.
x 240 pix.
= 548.16 Å
2.28 Å/pix.
x 240 pix.
= 548.16 Å
2.28 Å/pix.
x 240 pix.
= 548.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.284 Å
Density
Contour LevelBy AUTHOR: 0.44 / Movie #1: 0.44
Minimum - Maximum-0.51983 - 1.2029407
Average (Standard dev.)-0.00883188 (±0.08315184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 548.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2842.2842.284
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z548.160548.160548.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.5201.203-0.009

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Supplemental data

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Sample components

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Entire TFIID-based core PIC on CLAM2 promoter

EntireName: TFIID-based core PIC on CLAM2 promoter / Number of Components: 1

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Component #1: protein, TFIID-based core PIC on CLAM2 promoter

ProteinName: TFIID-based core PIC on CLAM2 promoter / Recombinant expression: No
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: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 50 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 8333
3D reconstructionResolution: 12 Å / Resolution Method: FSC 0.143 CUT-OFF

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