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- PDB-6mzl: Human TFIID canonical state -

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Basic information

Entry
Database: PDB / ID: 6mzl
TitleHuman TFIID canonical state
Components
  • (Transcription initiation factor TFIID subunit ...) x 14
  • (poly(UNK)) x 2
  • TATA-box-binding protein
KeywordsTRANSCRIPTION / Transcription / DNA / Nuclear
Function / homologyPeptidase M1 N-terminal domain / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 1, domain of unknown function / TATA-box binding protein, conserved site / TATA-box binding protein, eukaryotic / WD40-repeat-containing domain superfamily / Bromodomain-like superfamily / TAFII-230 TBP-binding domain superfamily / TAFH/NHR1 domain superfamily / TFIID subunit TAF5, NTD2 domain superfamily ...Peptidase M1 N-terminal domain / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 1, domain of unknown function / TATA-box binding protein, conserved site / TATA-box binding protein, eukaryotic / WD40-repeat-containing domain superfamily / Bromodomain-like superfamily / TAFII-230 TBP-binding domain superfamily / TAFH/NHR1 domain superfamily / TFIID subunit TAF5, NTD2 domain superfamily / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 3 / Zinc finger, PHD-finger / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 8 / Transcription initiation factor TFIID subunit 1 / Transcription factor TFIID (or TATA-binding protein, TBP) / WD domain, G-beta repeat / Bromodomain / PHD-finger / Transcription initiation factor IID, 18kD subunit / Zinc finger, PHD-type / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID subunit A / G-protein beta WD-40 repeat / Zinc finger, PHD-type, conserved site / TAFII55 protein conserved region / TAFII-230 TBP-binding / Transcription initiation factor IID, subunit 13 / Transcription initiation factor TFIID subunit 12 domain / TAFH/NHR1 / Transcription initiation factor TFIID, 23-30kDa subunit / TATA box binding protein associated factor (TAF) / Bromodomain associated domain / WD40 repeat / LIS1 homology motif / TAFII55 protein, conserved region / TAFII28-like protein / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID component TAF4 / Histone-fold / WD40 repeat, conserved site / Zinc finger, FYVE/PHD-type / Bromodomain / Transcription initiation factor TFIID subunit 1, animal / TAF6, C-terminal HEAT repeat domain / TBP domain superfamily / Zinc finger, RING/FYVE/PHD-type / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / TATA-box binding protein / WD40-repeat-containing domain / Bromodomain, conserved site / Transcription factor TFIID, subunit 8, C-terminal / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor IID, 31kD subunit / hTAFII28-like protein conserved region / RNA Polymerase II Promoter Escape / HATs acetylate histones / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Ub-specific processing proteases / RNA Polymerase II Pre-transcription Events / Transcription initiation factor TFIID component TAF4 family / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Chain Elongation / RNA Polymerase II HIV Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / 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 / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Estrogen-dependent gene expression / Zinc knuckle / Transcription of the HIV genome / Regulation of TP53 Activity through Phosphorylation / HIV Transcription Initiation / Zinc finger PHD-type signature. / Bromodomain associated / NHR1 homology to TAF / TAF6 C-terminal HEAT repeat domain / TATA box-binding protein binding / Transcription factor TFIID complex subunit 8 C-term / Protein of unknown function (DUF3591) / Bromodomain signature. / Trp-Asp (WD) repeats signature. / Transcription factor TFIID repeat signature. / Transcription initiation factor TAFII31 / TAFH/NHR1 domain profile. / LIS1 homology (LisH) motif profile. / Bromodomain profile.
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 23 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, chemical cross-linking mass spectrometry, 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
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 28, 2018Structure modelrepositoryInitial release
1.1Jan 2, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation_author.identifier_ORCID

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 1
B: Transcription initiation factor TFIID subunit 2
C: Transcription initiation factor TFIID subunit 3
D: Transcription initiation factor TFIID subunit 4
E: Transcription initiation factor TFIID subunit 4
F: Transcription initiation factor TFIID subunit 5,TAF5
G: Transcription initiation factor TFIID subunit 5,TAF5
H: Transcription initiation factor TFIID subunit 6
I: Transcription initiation factor TFIID subunit 6
J: Transcription initiation factor TFIID subunit 7
K: Transcription initiation factor TFIID subunit 8,TAF8
L: Transcription initiation factor TFIID subunit 9, TAF9
M: Transcription initiation factor TFIID subunit 9, TAF9
N: Transcription initiation factor TFIID subunit 10
O: Transcription initiation factor TFIID subunit 10
P: Transcription initiation factor TFIID subunit 11
Q: Transcription initiation factor TFIID subunit 12
R: Transcription initiation factor TFIID subunit 12
S: Transcription initiation factor TFIID subunit 13
T: TATA-box-binding protein
Y: poly(UNK)
Z: poly(UNK)


Theoretical massNumber of molelcules
Total (without water)1,305,17422
Polyers1,305,17422
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation, mass spectrometry
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TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Transcription initiation factor TFIID subunit ... , 14 types, 19 molecules ABCDEFGHIJKLMNOPQRS

#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: 212956.172 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Production host: Escherichia coli (E. coli)
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Protein/peptide Transcription initiation factor TFIID subunit 2 / 150 kDa cofactor of initiator function / RNA polymerase II TBP-associated factor subunit B


Mass: 137159.984 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P1X5
#3: Protein/peptide Transcription initiation factor TFIID subunit 3


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


Mass: 110221.883 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: O00268
#5: Protein/peptide Transcription initiation factor TFIID subunit 5,TAF5 / Transcription initiation factor TFIID 100 kDa subunit / TAFII100


Mass: 85785.164 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15542
#6: Protein/peptide Transcription initiation factor TFIID subunit 6 / RNA polymerase II TBP-associated factor subunit E


Mass: 72749.297 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P49848
#7: Protein/peptide Transcription initiation factor TFIID subunit 6 / RNA polymerase II TBP-associated factor subunit E / Transcription initiation factor TFIID 70 kDa subunit


Mass: 72365.836 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P49848
#8: Protein/peptide Transcription initiation factor TFIID subunit 7 / RNA polymerase II TBP-associated factor subunit F / Transcription initiation factor TFIID 55 kDa subunit / TAFII55


Mass: 40325.117 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15545
#9: Protein/peptide Transcription initiation factor TFIID subunit 8,TAF8 / Protein taube nuss / TBP-associated factor 43 kDa / TBP-associated factor 8 / Transcription initiation factor TFIID 43 kDa subunit / hTAFII43 / Protein taube nuss / TBP-associated factor 43 kDa


Mass: 32975.344 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7C8
#10: Protein/peptide Transcription initiation factor TFIID subunit 9, TAF9 / 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 / TAFII32


Mass: 28830.689 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: Q16594
#11: Protein/peptide Transcription initiation factor TFIID subunit 10 / STAF28 / Transcription initiation factor TFIID 30 kDa subunit / TAFII30


Mass: 21731.248 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: Q12962
#12: 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
#13: 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.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: Q16514
#14: 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 , 3 types, 3 molecules TYZ

#15: 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
#16: Protein/peptide poly(UNK)


Mass: 8188.084 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
#17: Protein/peptide poly(UNK)


Mass: 20272.906 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, 13, 14, 15, 16, 17
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

EM software
IDNameCategory
2Leginonimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 23 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 107900 / Symmetry type: POINT

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