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- PDB-6mzd: Human TFIID Lobe A canonical -

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Basic information

Entry
Database: PDB / ID: 6mzd
TitleHuman TFIID Lobe A canonical
Components
  • (Transcription initiation factor TFIID subunit ...) x 10
  • TATA-box-binding protein
  • poly(UNK)
KeywordsTRANSCRIPTION / Transcription / DNA / Nuclear
Function / homologyZinc knuckle / PHD-finger / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 3 / Bromodomain associated domain / Transcription factor TFIID (or TATA-binding protein, TBP) / WD domain, G-beta repeat / TATA box binding protein associated factor (TAF) ...Zinc knuckle / PHD-finger / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 3 / Bromodomain associated domain / Transcription factor TFIID (or TATA-binding protein, TBP) / WD domain, G-beta repeat / TATA box binding protein associated factor (TAF) / Bromodomain / Transcription initiation factor TFIID, 23-30kDa subunit / TAFH/NHR1 domain superfamily / Transcription initiation factor IID, 18kD subunit / Transcription initiation factor IID, 31kD subunit / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID subunit A / WD40 associated region in TFIID subunit, NTD2 domain / hTAFII28-like protein conserved region / Transcription initiation factor TFIID component TAF4 family / Bromodomain associated / TFIID subunit TAF5, NTD2 domain superfamily / TAFII-230 TBP-binding domain superfamily / TAF6 C-terminal HEAT repeat domain / WD40-repeat-containing domain / Transcription initiation factor TFIID subunit 1, animal / TAF6, C-terminal HEAT repeat domain / TBP domain superfamily / TAFII-230 TBP-binding / Zinc finger, RING/FYVE/PHD-type / Transcription initiation factor TFIID component TAF4 / WD40/YVTN repeat-like-containing domain superfamily / TFIID subunit TAF5, NTD2 domain / Armadillo-type fold / Bromodomain, conserved site / Bromodomain-like superfamily / WD40 repeat, conserved site / Zinc finger, PHD-type, conserved site / TAFII28-like protein / Zinc finger, PHD-finger / G-protein beta WD-40 repeat / Transcription initiation factor TFIID subunit 1, domain of unknown function / TATA-box binding protein, conserved site / TATA-box binding protein, eukaryotic / LIS1 homology motif / WD40-repeat-containing domain superfamily / NHR1 homology to TAF / TATA box-binding protein binding / Histone-fold / WD40 repeat / RNA polymerase II transcribes snRNA genes / Transcription initiation factor TAFII31 / Zinc finger, PHD-type / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Promoter Escape / RNA Polymerase I Chain Elongation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / Bromodomain / RNA Polymerase II Pre-transcription Events / RNA Polymerase I Transcription Termination / RNA Polymerase III Abortive And Retractive Initiation / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / TATA-box binding protein / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Estrogen-dependent gene expression / Protein of unknown function (DUF3591) / Regulation of TP53 Activity through Phosphorylation / Ub-specific processing proteases / B-WICH complex positively regulates rRNA expression / TAFH/NHR1 / Transcription initiation factor TFIID subunit 12 domain / Transcription factor TFIID repeat signature. / Bromodomain signature. / Trp-Asp (WD) repeats signature. / Zinc finger PHD-type signature. / Bromodomain profile. / Zinc finger PHD-type profile. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / LIS1 homology (LisH) motif profile. / Transcription initiation factor IID, subunit 13 / TAFH/NHR1 domain profile. / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / HATs acetylate histones / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Zinc finger, FYVE/PHD-type / negative regulation of protein autoubiquitination / regulation of transcription initiation from RNA polymerase II promoter / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / pre-snoRNP complex / regulation of cell cycle G1/S phase transition / negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9.8 Å resolution
AuthorsPatel, A.B. / Louder, R.K. / Greber, B.J. / 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 Report
SummaryFull reportAbout validation report
DateDeposition: Nov 5, 2018 / Release: Nov 28, 2018

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Structure visualization

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 1
C: Transcription initiation factor TFIID subunit 3
D: Transcription initiation factor TFIID subunit 4
F: Transcription initiation factor TFIID subunit 5
H: Transcription initiation factor TFIID subunit 6
L: Transcription initiation factor TFIID subunit 9
N: Transcription initiation factor TFIID subunit 10
P: Transcription initiation factor TFIID subunit 11
Q: Transcription initiation factor TFIID subunit 12
S: Transcription initiation factor TFIID subunit 13
T: TATA-box-binding protein
Y: poly(UNK)


Theoretical massNumber of molelcules
Total (without water)737,65112
Polyers737,65112
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation, mass spectrometry
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TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Transcription initiation factor TFIID subunit ... , 10 types, 10 molecules ACDFHLNPQS

#1: Protein/peptide Transcription initiation factor TFIID subunit 1 / Cell cycle gene 1 protein / TBP-associated factor 250 kDa / p250 / Transcription initiation factor TFIID 250 kDa subunit / TAFII250


Mass: 213050.125 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Protein/peptide Transcription initiation factor TFIID subunit 3 / 140 kDa TATA box-binding protein-associated factor / TBP-associated factor 3 / Transcription initiation factor TFIID 140 kDa subunit / TAFII140


Mass: 103769.320 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q5VWG9
#3: Protein/peptide Transcription initiation factor TFIID subunit 4 / RNA polymerase II TBP-associated factor subunit C / TBP-associated factor 4 / Transcription initiation factor TFIID 130 kDa subunit / TAFII130 / Transcription initiation factor TFIID 135 kDa subunit / TAFII135


Mass: 110221.883 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O00268
#4: Protein/peptide Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID 100 kDa subunit / TAFII100


Mass: 85785.164 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15542
#5: Protein/peptide Transcription initiation factor TFIID subunit 6 / RNA polymerase II TBP-associated factor subunit E / Transcription initiation factor TFIID 70 kDa subunit / TAFII70 / Transcription initiation factor TFIID 80 kDa subunit / TAFII80


Mass: 72749.297 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P49848
#6: Protein/peptide Transcription initiation factor TFIID subunit 9 / RNA polymerase II TBP-associated factor subunit G / STAF31/32 / Transcription initiation factor TFIID 31 kDa subunit / TAFII31 / Transcription initiation factor TFIID 32 kDa subunit


Mass: 28830.689 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q16594
#7: Protein/peptide Transcription initiation factor TFIID subunit 10 / STAF28 / Transcription initiation factor TFIID 30 kDa subunit / TAFII30


Mass: 21731.248 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q12962
#8: Protein/peptide Transcription initiation factor TFIID subunit 11 / TFIID subunit p30-beta / Transcription initiation factor TFIID 28 kDa subunit / TAFII28


Mass: 23340.094 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15544
#9: Protein/peptide Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID 20/15 kDa subunits / TAFII20/TAFII15


Mass: 17948.467 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q16514
#10: Protein/peptide Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID 18 kDa subunit / TAFII18


Mass: 14307.068 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15543

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Protein/peptide , 2 types, 2 molecules TY

#11: Protein/peptide TATA-box-binding protein / TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation factor TFIID TBP subunit


Mass: 37729.938 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P20226
#12: Protein/peptide poly(UNK)


Mass: 8188.084 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: General transcription factor IID / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa
Buffer solutionpH: 7.9
Buffer component
IDConc.FormulaBuffer ID
120 mMHEPES1
2.1 mMEDTA1
35 mMMgCl1
42 %Glycerol1
51 %Trehalose1
6100 mMKCl1
7.01 %NP-401
SpecimenConc.: .2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins / Details: BT 4s; BF 15N

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 50 microns
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3211: / Classification: refinement
EM software
IDNameCategory
1Gautomatchparticle selection
2Leginonimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 107900 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411324
ELECTRON MICROSCOPYf_angle_d0.97415355
ELECTRON MICROSCOPYf_dihedral_angle_d4.9696855
ELECTRON MICROSCOPYf_chiral_restr0.0561772
ELECTRON MICROSCOPYf_plane_restr0.0061995

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