+Open data
-Basic information
Entry | Database: PDB / ID: 6mzd | |||||||||
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Title | Human TFIID Lobe A canonical | |||||||||
Components |
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Keywords | TRANSCRIPTION / DNA / Nuclear | |||||||||
Function / homology | Function and homology information SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / pre-snoRNP complex / negative regulation of protein autoubiquitination / transcription factor TFTC complex / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity ...SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / pre-snoRNP complex / negative regulation of protein autoubiquitination / transcription factor TFTC complex / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase transcription factor SL1 complex / RNA polymerase I core promoter sequence-specific DNA binding / hepatocyte differentiation / 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 / positive regulation of response to cytokine stimulus / positive regulation of androgen receptor activity / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / C2H2 zinc finger domain binding / male pronucleus / female pronucleus / positive regulation by host of viral transcription / transcription regulator inhibitor activity / nuclear vitamin D receptor binding / RNA polymerase binding / box C/D snoRNP assembly / RNA polymerase II general transcription initiation factor binding / SAGA complex / limb development / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / response to L-glutamate / cellular response to ATP / midbrain development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 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 / RNA Polymerase I Transcription Initiation / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / aryl hydrocarbon receptor binding / regulation of RNA splicing / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / MLL1 complex / transcription factor TFIID complex / TFIIB-class transcription factor binding / negative regulation of cell cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA polymerase II general transcription initiation factor activity / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / somitogenesis / positive regulation of intrinsic apoptotic signaling pathway / core promoter sequence-specific DNA binding / ovarian follicle development / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / negative regulation of ubiquitin-dependent protein catabolic process / response to interleukin-1 / SIRT1 negatively regulates rRNA expression / regulation of signal transduction by p53 class mediator / male germ cell nucleus / DNA-templated transcription initiation / promoter-specific chromatin binding / nuclear receptor binding / nuclear estrogen receptor binding / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / euchromatin / lysine-acetylated histone binding / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / multicellular organism growth / negative regulation of DNA-binding transcription factor activity / G1/S transition of mitotic cell cycle / protein polyubiquitination / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / actin cytoskeleton / positive regulation of protein binding / kinase activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.8 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 | 6mzd.cif.gz | 360.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mzd.ent.gz | 227.3 KB | Display | PDB format |
PDBx/mmJSON format | 6mzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mzd_validation.pdf.gz | 830.8 KB | Display | wwPDB validaton report |
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Full document | 6mzd_full_validation.pdf.gz | 843 KB | Display | |
Data in XML | 6mzd_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 6mzd_validation.cif.gz | 64.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/6mzd ftp://data.pdbj.org/pub/pdb/validation_reports/mz/6mzd | HTTPS FTP |
-Related structure data
Related structure data | 9302MC 9298C 9299C 9300C 9301C 9305C 9306C 6mzcC 6mzlC 6mzmC C: citing same article (ref.) M: map data used to model this data |
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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 ... , 10 types, 10 molecules ACDFHLNPQS
#1: Protein | Mass: 213050.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 103769.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5VWG9 |
#3: Protein | Mass: 110221.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00268 |
#4: Protein | Mass: 85785.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15542 |
#5: Protein | Mass: 72749.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49848 |
#6: Protein | Mass: 28830.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16594 |
#7: Protein | Mass: 21731.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12962 |
#8: Protein | Mass: 23340.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15544 |
#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 |
#10: Protein | Mass: 14307.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15543 |
-Protein , 2 types, 2 molecules TY
#11: Protein | Mass: 37729.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P20226 |
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#12: Protein | Mass: 8188.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-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 | ||||||||||||||||||||||||||||||||
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 FIELD / 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 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107900 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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