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- EMDB-31133: PUMA promoter-bound TFIID-TFIIA -

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Basic information

Entry
Database: EMDB / ID: EMD-31133
TitlePUMA promoter-bound TFIID-TFIIA
Map data
SamplePUMA promoter-bound TFIID-TFIIA
Function / homology
Function and homology information


spermine transport / negative regulation of MHC class I biosynthetic process / Formation of the Early Elongation Complex / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Minor Pathway / RNA polymerase II transcribes snRNA genes / mRNA Splicing - Major Pathway / mRNA Capping / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / FGFR2 alternative splicing ...spermine transport / negative regulation of MHC class I biosynthetic process / Formation of the Early Elongation Complex / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Minor Pathway / RNA polymerase II transcribes snRNA genes / mRNA Splicing - Major Pathway / mRNA Capping / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / FGFR2 alternative splicing / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation by small RNAs / RNA Polymerase II Promoter Escape / TFIIH-class transcription factor complex binding / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Formation of RNA Pol II elongation complex / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / pre-snoRNP complex / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / 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 / STAGA complex / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / RNA polymerase II core complex assembly / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / PCAF complex / regulation of cell cycle G1/S phase transition / phosphatase activator activity / TFIIF-class transcription factor complex binding / SLIK (SAGA-like) complex / RNA polymerase I general transcription initiation factor activity / positive regulation of core promoter binding / transcription factor TFIIF complex / regulation of DNA binding / transcriptional start site selection at RNA polymerase II promoter / transcription regulator inhibitor activity / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / SAGA complex / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of response to cytokine stimulus / inner cell mass cell proliferation / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / RNA polymerase III general transcription initiation factor activity / maintenance of protein location in nucleus / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of androgen receptor activity / histone deubiquitination / hepatocyte differentiation / general transcription initiation factor activity / RNA Polymerase I Transcription Termination / box C/D snoRNP assembly / transcription factor catabolic process / RNA polymerase II general transcription initiation factor binding / negative regulation of histone acetylation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / C2H2 zinc finger domain binding / Formation of the Early Elongation Complex / positive regulation by host of viral transcription / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / FGFR2 alternative splicing / male pronucleus / female pronucleus / Viral Messenger RNA Synthesis / positive regulation of viral transcription / RNA polymerase binding / RNA polymerase II preinitiation complex assembly / transcription initiation from RNA polymerase I promoter / thyroid hormone receptor binding / Processing of Capped Intron-Containing Pre-mRNA / vitamin D receptor binding / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / midbrain development / RNA Polymerase II HIV Promoter Escape / RNA polymerase complex / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation And Promoter Clearance / HIV Transcription Initiation / Transcription of the HIV genome / Tat-mediated HIV elongation arrest and recovery / Pausing and recovery of Tat-mediated HIV elongation / regulation of fat cell differentiation / termination of RNA polymerase I transcription / Pausing and recovery of HIV elongation / HIV elongation arrest and recovery / RNA polymerase II activity
Similarity search - Function
hTAFII28-like protein conserved region / TAFII28-like protein / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein, conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal ...hTAFII28-like protein conserved region / TAFII28-like protein / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein, conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 2 / 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 IID, 18kD subunit / Transcription initiation factor IID, subunit 13 / Transcription initiation factor TFIID component TAF4 / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAFH/NHR1 domain superfamily / TAF homology / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Transcription initiation factor IID, 31kD subunit / Bromodomain associated domain / Transcription initiation factor TFIID subunit 5 / TAFH/NHR1 / Transcription initiation factor TFIID subunit A / Transcription initiation factor TFIID subunit 12 / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TAFII31 / TATA box binding protein associated factor (TAF) / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 12 domain / TAF6 C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 6 / TAFII-230 TBP-binding / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Transcription initiation factor TFIID subunit 1, animal / TAF6, C-terminal HEAT repeat domain / Zinc knuckle / Transcription initiation factor TFIID 23-30kDa subunit / Zinc knuckle / Transcription initiation factor TFIID subunit 1, domain of unknown function / Protein of unknown function (DUF3591) / Transcription initiation factor TFIID subunit 1 / Transcription initiation factor TFIID, 23-30kDa subunit / TFIIF, beta subunit, N-terminal / TFIIF beta subunit, HTH domain / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription initiation factor IIF, alpha subunit / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Transcription factor TFIIB repeat / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB, cyclin-like domain / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / TFIIB zinc-binding / Zinc finger, TFIIB-type / TATA-box binding protein, eukaryotic / Transcription factor TFIID (or TATA-binding protein, TBP) / TATA-box binding protein, conserved site / TATA-box binding protein / Transcription factor TFIID repeat signature. / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb4/RPC9, core / TBP domain superfamily / Rpb4/RPC9 superfamily / RNA polymerase RBP11 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase subunit RPB4/RPC9 / Aminopeptidase N-like , N-terminal / RNA polymerase Rpb4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like, N-terminal domain superfamily / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like / Cyclin-like superfamily
Similarity search - Domain/homology
Transcription initiation factor IIA subunit 1 / Transcription initiation factor TFIID subunit 13 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 9 ...Transcription initiation factor IIA subunit 1 / Transcription initiation factor TFIID subunit 13 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 3 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor IIA subunit 2 / RNA_pol_L_2 domain-containing protein / Transcription initiation factor TFIID subunit 6 / General transcription factor IIF subunit 1 / 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 / 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: 7.85 Å
AuthorsChen X / Wu Z / Li J / Zhao D / Wang X / Qi Y / Hou H / 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 21, 2021-
Map releaseApr 21, 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: 0.005
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

FileDownload / File: emd_31133.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 384 pix.
= 518.4 Å
1.35 Å/pix.
x 384 pix.
= 518.4 Å
1.35 Å/pix.
x 384 pix.
= 518.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.0080610365 - 0.03656554
Average (Standard dev.)5.263576e-06 (±0.0011941555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 518.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z518.400518.400518.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0080.0370.000

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Supplemental data

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Sample components

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Entire PUMA promoter-bound TFIID-TFIIA

EntireName: PUMA promoter-bound TFIID-TFIIA / Number of components: 1

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Component #1: protein, PUMA promoter-bound TFIID-TFIIA

ProteinName: PUMA promoter-bound TFIID-TFIIA / 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: 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
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 106635
3D reconstructionResolution: 7.85 Å / Resolution method: FSC 0.143 CUT-OFF

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