+Open data
-Basic information
Entry | Database: PDB / ID: 6mzm | |||||||||
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Title | Human TFIID bound to promoter DNA and TFIIA | |||||||||
Components |
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Keywords | transcription/dna / Transcription / DNA / Nuclear / transcription-dna complex | |||||||||
Function / homology | Function and homology information spermine transport / negative regulation of MHC class I biosynthetic process / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / TFIIH-class transcription factor complex binding / pre-snoRNP complex / negative regulation of protein autoubiquitination / transcription factor TFTC complex ...spermine transport / negative regulation of MHC class I biosynthetic process / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / TFIIH-class transcription factor complex binding / pre-snoRNP complex / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / RNA polymerase transcription factor SL1 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 / hepatocyte differentiation / maintenance of protein location in nucleus / 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 / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / C2H2 zinc finger domain binding / male pronucleus / female pronucleus / transcription regulator inhibitor activity / box C/D snoRNP assembly / nuclear vitamin D receptor binding / RNA polymerase binding / SAGA complex / RNA polymerase II general transcription initiation factor binding / limb development / transcription preinitiation complex / nuclear thyroid hormone receptor binding / RNA Polymerase I Transcription Termination / regulation of fat cell differentiation / inner cell mass cell proliferation / response to L-glutamate / cellular response to ATP / histone acetyltransferase binding / midbrain development / RNA polymerase II general transcription initiation factor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / transcription factor TFIID complex / 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 / ubiquitin conjugating enzyme activity / regulation of RNA splicing / RNA Polymerase I Transcription Initiation / transcription initiation at RNA polymerase I promoter / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / MLL1 complex / TFIIB-class transcription factor binding / P-TEFb complex binding / 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 / RNA polymerase II core promoter sequence-specific DNA binding / intracellular estrogen receptor signaling pathway / transcription by RNA polymerase III / regulation of DNA repair / somitogenesis / positive regulation of intrinsic apoptotic signaling pathway / core promoter sequence-specific DNA binding / ovarian follicle development / RNA polymerase II preinitiation complex assembly / histone acetyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / response to interleukin-1 / SIRT1 negatively regulates rRNA expression / regulation of signal transduction by p53 class mediator / male germ cell nucleus / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / nuclear receptor binding / RNA Polymerase I Promoter Escape / peptidyl-threonine phosphorylation / G1/S transition of mitotic cell cycle / negative regulation of protein kinase activity / multicellular organism growth / lysine-acetylated histone binding / euchromatin / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 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 | 6mzm.cif.gz | 778.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mzm.ent.gz | 560 KB | Display | PDB format |
PDBx/mmJSON format | 6mzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/6mzm ftp://data.pdbj.org/pub/pdb/validation_reports/mz/6mzm | HTTPS FTP |
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-Related structure data
Related structure data | 9306MC 9298C 9299C 9300C 9301C 9302C 9305C 6mzcC 6mzdC 6mzlC 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 ... , 11 types, 11 molecules ABDGHIJKLOR
#1: Protein | Mass: 57193.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P21675*PLUS |
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#2: Protein | Mass: 137159.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P1X5 |
#3: Protein | Mass: 104052.086 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: 72365.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49848 |
#7: Protein | Mass: 40325.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15545 |
#8: Protein | Mass: 32975.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7C8 |
#9: Protein | Mass: 28830.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16594 |
#10: Protein | Mass: 21731.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12962 |
#11: 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 , 2 types, 2 molecules TZ
#12: 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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#17: Protein | Mass: 20272.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-DNA chain , 2 types, 2 molecules UV
#13: DNA chain | Mass: 24498.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#14: DNA chain | Mass: 24854.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Transcription initiation factor IIA subunit ... , 2 types, 2 molecules WX
#15: Protein | Mass: 10675.194 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A1, TF2A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52655*PLUS |
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#16: Protein | Mass: 11275.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A2, TF2A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52657 |
-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 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: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25180 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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