+Open data
-Basic information
Entry | Database: PDB / ID: 6mzl | |||||||||
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Title | Human TFIID canonical state | |||||||||
Components |
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Keywords | TRANSCRIPTION / DNA / Nuclear | |||||||||
Function / homology | Function and homology information spermine transport / negative regulation of MHC class I biosynthetic process / P-TEFb complex binding / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination ...spermine transport / negative regulation of MHC class I biosynthetic process / P-TEFb complex binding / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / regulation of cell cycle G1/S phase transition / RNA polymerase transcription factor SL1 complex / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / 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 / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / positive regulation of androgen receptor activity / 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 / RNA polymerase II general transcription initiation factor binding / limb development / box C/D snoRNP assembly / regulation of fat cell differentiation / nuclear thyroid hormone receptor binding / SAGA complex / transcription preinitiation complex / RNA Polymerase I Transcription Termination / inner cell mass cell proliferation / response to L-glutamate / embryonic placenta development / cellular response to ATP / midbrain development / histone acetyltransferase binding / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 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 / regulation of RNA splicing / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / aryl hydrocarbon receptor binding / transcription by RNA polymerase III / TFIIB-class transcription factor binding / RNA polymerase II transcribes snRNA genes / MLL1 complex / negative regulation of cell cycle / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / estrogen receptor signaling pathway / male germ cell nucleus / negative regulation of ubiquitin-dependent protein catabolic process / somitogenesis / regulation of DNA repair / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / RNA polymerase II preinitiation complex assembly / histone acetyltransferase activity / histone acetyltransferase / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / lysine-acetylated histone binding / 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 / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / RNA Polymerase I Promoter Escape / nuclear receptor binding / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 23 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 | 6mzl.cif.gz | 925.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mzl.ent.gz | 670.9 KB | Display | PDB format |
PDBx/mmJSON format | 6mzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mzl_validation.pdf.gz | 950.4 KB | Display | wwPDB validaton report |
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Full document | 6mzl_full_validation.pdf.gz | 1011.1 KB | Display | |
Data in XML | 6mzl_validation.xml.gz | 113.6 KB | Display | |
Data in CIF | 6mzl_validation.cif.gz | 183.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/6mzl ftp://data.pdbj.org/pub/pdb/validation_reports/mz/6mzl | HTTPS FTP |
-Related structure data
Related structure data | 9305MC 9298C 9299C 9300C 9301C 9302C 9306C 6mzcC 6mzdC 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 ... , 14 types, 19 molecules ABCDEFGHIJKLMNOPQRS
#1: Protein | Mass: 212956.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source 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 | ||||||||||||||||||||
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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: 103769.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5VWG9 | ||||||||||||||||||||
#4: Protein | Mass: 110221.883 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00268 #5: Protein | Mass: 85785.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15542 #6: Protein | | Mass: 72749.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49848 #7: Protein | | Mass: 72365.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49848 #8: Protein | | Mass: 40325.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15545 #9: Protein | | Mass: 32975.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7C8 #10: Protein | Mass: 28830.689 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16594 #11: Protein | Mass: 21731.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12962 #12: Protein | | Mass: 23340.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15544 #13: Protein | Mass: 17948.467 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16514 #14: 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 , 3 types, 3 molecules TYZ
#15: 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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#16: Protein | Mass: 8188.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#17: Protein | Mass: 20272.906 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
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||
3D reconstruction | Resolution: 23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107900 / Symmetry type: POINT |