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- PDB-6mzc: Human TFIID BC core -

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Basic information

Entry
Database: PDB / ID: 6mzc
TitleHuman TFIID BC core
Components
  • (Transcription initiation factor TFIID subunit ...) x 9
  • poly(UNK)
KeywordsTRANSCRIPTION / Transcription / DNA / Nuclear
Function / homologyPeptidase M1 N-terminal domain / Armadillo-type fold / Transcription initiation factor TFIID subunit 8 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 5 / TFIID subunit TAF5, NTD2 domain superfamily / TAFH/NHR1 domain superfamily / WD40-repeat-containing domain superfamily ...Peptidase M1 N-terminal domain / Armadillo-type fold / Transcription initiation factor TFIID subunit 8 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 5 / TFIID subunit TAF5, NTD2 domain superfamily / TAFH/NHR1 domain superfamily / WD40-repeat-containing domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Transcription factor TFIID, subunit 8, C-terminal / WD40-repeat-containing domain / WD40/YVTN repeat-like-containing domain superfamily / TATA box binding protein associated factor (TAF) / TAF6, C-terminal HEAT repeat domain / Histone-fold / Transcription initiation factor TFIID component TAF4 / TFIID subunit TAF5, NTD2 domain / LIS1 homology motif / Bromodomain associated domain / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID, 23-30kDa subunit / TAFH/NHR1 / Transcription initiation factor TFIID subunit 12 domain / Transcription initiation factor TAFII31 / WD40 repeat / Transcription initiation factor IID, 31kD subunit / WD domain, G-beta repeat / Transcription initiation factor TFIID 23-30kDa subunit / TAFH/NHR1 domain profile. / 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 / RNA polymerase II transcribes snRNA genes / Regulation of TP53 Activity through Phosphorylation / RNA Polymerase II Pre-transcription Events / Ub-specific processing proteases / HATs acetylate histones / Transcription of the HIV genome / Transcription initiation factor TFIID subunit A / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / NHR1 homology to TAF / WD40 associated region in TFIID subunit, NTD2 domain / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats signature. / Transcription factor TFIID complex subunit 8 C-term / TAF6 C-terminal HEAT repeat domain / LIS1 homology (LisH) motif profile. / Bromodomain associated / Transcription initiation factor TFIID component TAF4 family / pre-snoRNP complex / STAGA complex / transcription factor TFTC complex / inner cell mass cell proliferation / PCAF complex / SLIK (SAGA-like) complex / regulation of DNA binding / maintenance of protein location in nucleus / SAGA complex / positive regulation of response to cytokine stimulus / histone deubiquitination / hepatocyte differentiation / regulation of fat cell differentiation / C2H2 zinc finger domain binding / box C/D snoRNP assembly / RNA polymerase II preinitiation complex assembly / snRNA transcription by RNA polymerase II / RNA polymerase binding / MLL1 complex / transcription factor TFIID complex / positive regulation of transcription initiation from RNA polymerase II promoter / cellular protein-containing complex assembly / TFIID-class transcription factor complex binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of cell cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / response to interleukin-1 / regulation of DNA-binding transcription factor activity / histone acetylation / RNA polymerase II activating transcription factor binding / DNA-templated transcription, initiation / activating transcription factor binding / ovarian follicle development / positive regulation of intrinsic apoptotic signaling pathway / thiol-dependent ubiquitinyl hydrolase activity / aryl hydrocarbon receptor binding / histone H3 acetylation / TBP-class protein binding / multicellular organism growth / G1/S transition of mitotic cell cycle / estrogen receptor binding / actin cytoskeleton / response to organic cyclic compound / p53 binding / chromatin organization
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 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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Assembly

Deposited unit
B: Transcription initiation factor TFIID subunit 2
E: Transcription initiation factor TFIID subunit 4
G: Transcription initiation factor TFIID subunit 5
H: Transcription initiation factor TFIID subunit 6
I: Transcription initiation factor TFIID subunit 6
K: Transcription initiation factor TFIID subunit 8
M: Transcription initiation factor TFIID subunit 9
O: Transcription initiation factor TFIID subunit 10
R: Transcription initiation factor TFIID subunit 12
Z: poly(UNK)


Theoretical massNumber of molelcules
Total (without water)600,04110
Polyers600,04110
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 ... , 9 types, 9 molecules BEGHIKMOR

#1: Protein/peptide Transcription initiation factor TFIID subunit 2 / 150 kDa cofactor of initiator function / RNA polymerase II TBP-associated factor subunit B / TBP-associated factor 150 kDa


Mass: 137159.984 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q6P1X5
#2: 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


Mass: 110221.883 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O00268
#3: 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
#4: 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
#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


Mass: 72365.836 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P49848
#6: Protein/peptide Transcription initiation factor TFIID subunit 8 / Protein taube nuss / TBP-associated factor 43 kDa


Mass: 32975.344 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7C8
#7: 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
#8: 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
#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

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Protein/peptide , 1 types, 1 molecules Z

#10: 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 / 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
Specimen supportDetails: Treated with PEI
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
2Leginonimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 266328 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01021660
ELECTRON MICROSCOPYf_angle_d1.29129451
ELECTRON MICROSCOPYf_dihedral_angle_d8.06713060
ELECTRON MICROSCOPYf_chiral_restr0.0653434
ELECTRON MICROSCOPYf_plane_restr0.0093799

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