+Open data
-Basic information
Entry | Database: PDB / ID: 6mzc | |||||||||
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Title | Human TFIID BC core | |||||||||
Components |
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Keywords | TRANSCRIPTION / DNA / Nuclear | |||||||||
Function / homology | Function and homology information SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / transcription factor TFTC complex / SLIK (SAGA-like) complex / positive regulation of response to cytokine stimulus / hepatocyte differentiation / maintenance of protein location in nucleus ...SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / transcription factor TFTC complex / SLIK (SAGA-like) complex / positive regulation of response to cytokine stimulus / hepatocyte differentiation / maintenance of protein location in nucleus / C2H2 zinc finger domain binding / box C/D snoRNP assembly / SAGA complex / RNA polymerase binding / limb development / transcription preinitiation complex / regulation of fat cell differentiation / response to L-glutamate / inner cell mass cell proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / regulation of RNA splicing / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / MLL1 complex / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cell cycle / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / regulation of DNA repair / somitogenesis / ovarian follicle development / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / positive regulation of intrinsic apoptotic signaling pathway / response to interleukin-1 / male germ cell nucleus / promoter-specific chromatin binding / nuclear estrogen receptor binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / multicellular organism growth / G1/S transition of mitotic cell cycle / mRNA transcription by RNA polymerase II / response to organic cyclic compound / G2/M transition of mitotic cell cycle / actin cytoskeleton / p53 binding / HATs acetylate histones / ATPase binding / Regulation of TP53 Activity through Phosphorylation / DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / cell differentiation / transcription cis-regulatory region binding / protein stabilization / Ub-specific processing proteases / chromatin remodeling / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / apoptotic process / DNA damage response / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Patel, A.B. / Louder, R.K. / Greber, B.J. / Grunberg, S. / Luo, J. / Fang, J. / Liu, Y. / Ranish, J. / Hahn, S. / Nogales, E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6mzc.cif.gz | 534.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mzc.ent.gz | 399.6 KB | Display | PDB format |
PDBx/mmJSON format | 6mzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/6mzc ftp://data.pdbj.org/pub/pdb/validation_reports/mz/6mzc | HTTPS FTP |
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-Related structure data
Related structure data | 9298MC 9299C 9300C 9301C 9302C 9305C 9306C 6mzdC 6mzlC 6mzmC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Transcription initiation factor TFIID subunit ... , 9 types, 9 molecules BEGHIKMOR
#1: Protein | Mass: 137159.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q6P1X5 |
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#2: Protein | Mass: 110221.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00268 |
#3: Protein | Mass: 85785.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15542 |
#4: Protein | Mass: 72749.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49848 |
#5: Protein | Mass: 72365.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49848 |
#6: Protein | Mass: 32975.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7C8 |
#7: Protein | Mass: 28830.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16594 |
#8: Protein | Mass: 21731.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12962 |
#9: Protein | Mass: 17948.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16514 |
-Protein , 1 types, 1 molecules Z
#10: Protein | Mass: 20272.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: General transcription factor IID / Type: COMPLEX / Entity ID: all / Source: NATURAL | ||||||||||||||||||||||||||||||||
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Source (natural) | Organism: Homo sapiens (human) / Strain: HeLa | ||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||
Specimen support | Details: Treated with PEI | ||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: BT 4s; BF 15N |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3211: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266328 / Symmetry type: POINT | ||||||||||||||||||||||||
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