+Open data
-Basic information
Entry | Database: PDB / ID: 7kue | ||||||
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Title | CryoEM structure of Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex | ||||||
Components |
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Keywords | TRANSCRIPTION/Transferase / Polymerase CTD / TFIIH / Phosphorylation / Kinase / CDK / Cyclin / TRANSCRIPTION-Transferase complex | ||||||
Function / homology | Function and homology information positive regulation of Atg1/ULK1 kinase complex assembly / transcription factor TFIIK complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / [RNA-polymerase]-subunit kinase / cellular response to nitrogen starvation / cyclin-dependent protein serine/threonine kinase regulator activity / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping ...positive regulation of Atg1/ULK1 kinase complex assembly / transcription factor TFIIK complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / [RNA-polymerase]-subunit kinase / cellular response to nitrogen starvation / cyclin-dependent protein serine/threonine kinase regulator activity / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / 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 II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / Dual incision in TC-NER / 7-methylguanosine mRNA capping / cyclin-dependent protein serine/threonine kinase activity / positive regulation of autophagy / RNA polymerase II CTD heptapeptide repeat kinase activity / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription by RNA polymerase II / protein kinase activity / cell division / DNA repair / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | van Eeuwen, T. / Murakami, K. / Li, T. / Tsai, K.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2021 Title: Structure of TFIIK for phosphorylation of CTD of RNA polymerase II. Authors: Trevor van Eeuwen / Tao Li / Hee Jong Kim / Jose J Gorbea Colón / Mitchell I Parker / Roland L Dunbrack / Benjamin A Garcia / Kuang-Lei Tsai / Kenji Murakami / Abstract: During transcription initiation, the general transcription factor TFIIH marks RNA polymerase II by phosphorylating Ser5 of the carboxyl-terminal domain (CTD) of Rpb1, which is followed by extensive ...During transcription initiation, the general transcription factor TFIIH marks RNA polymerase II by phosphorylating Ser5 of the carboxyl-terminal domain (CTD) of Rpb1, which is followed by extensive modifications coupled to transcription elongation, mRNA processing, and histone dynamics. We have determined a 3.5-Å resolution cryo-electron microscopy (cryo-EM) structure of the TFIIH kinase module (TFIIK in yeast), which is composed of Kin28, Ccl1, and Tfb3, yeast homologs of CDK7, cyclin H, and MAT1, respectively. The carboxyl-terminal region of Tfb3 was lying at the edge of catalytic cleft of Kin28, where a conserved Tfb3 helix served to stabilize the activation loop in its active conformation. By combining the structure of TFIIK with the previous cryo-EM structure of the preinitiation complex, we extend the previously proposed model of the CTD path to the active site of TFIIK. | ||||||
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 | 7kue.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kue.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 7kue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kue_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7kue_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7kue_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 7kue_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/7kue ftp://data.pdbj.org/pub/pdb/validation_reports/ku/7kue | HTTPS FTP |
-Related structure data
Related structure data | 23036MC 6xi8C 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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-Components
#1: Protein | Mass: 38128.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q03290 |
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#2: Protein | Mass: 35369.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P06242, [RNA-polymerase]-subunit kinase |
#3: Protein | Mass: 45259.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P37366 |
#4: Chemical | ChemComp-ADP / |
#5: Chemical | ChemComp-AF3 / |
Has ligand of interest | N |
Has protein modification | Y |
-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: Ternary complex of Kin28-Ccl1-Tfb3 from Saccharomyces cerevisiae. Type: COMPLEX Details: the yeast Cdk7 complex, that phosphorylates the RNA pol II C-terminal domain (CTD) in transcription initiation. Entity ID: #1-#3 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.073 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 Tfb3-TAP | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM CPC / Cryogen name: ETHANE / Humidity: 0 % / Chamber temperature: 293 K Details: blotted for 2 seconds with Whatman 41 ashless filter paper |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.24 sec. / Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4620 Details: Images collected in super-resolution mode. Movies were 35 frames. Imaging 1 image/hole, image shift between 4 holes. Focus once per image shift |
EM imaging optics | Energyfilter name: GIF Bioquantum |
-Processing
Software | Name: PHENIX / Version: 1.18.1_3865: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: Movies collected in super resolution mode and binned during motion correction by MotionCorr2 | ||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3288475 Details: small particle set picked by blob used to generate 2D references used for large scale particle picking | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81466 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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