National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01-GM123233
United States
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
Deposition
Nov 24, 2020
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Header (metadata) release
Apr 28, 2021
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Map release
Apr 28, 2021
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Update
Apr 28, 2021
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Current status
Apr 28, 2021
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Entire : Ternary complex of Kin28-Ccl1-Tfb3 from Saccharomyces cerevisiae.
Entire
Name: Ternary complex of Kin28-Ccl1-Tfb3 from Saccharomyces cerevisiae.
Components
Complex: Ternary complex of Kin28-Ccl1-Tfb3 from Saccharomyces cerevisiae.
Protein or peptide: RNA polymerase II transcription factor B subunit 3
Protein or peptide: Serine/threonine-protein kinase KIN28
Protein or peptide: Cyclin CCL1
Ligand: ADENOSINE-5'-DIPHOSPHATE
Ligand: ALUMINUM FLUORIDE
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Supramolecule #1: Ternary complex of Kin28-Ccl1-Tfb3 from Saccharomyces cerevisiae.
Supramolecule
Name: Ternary complex of Kin28-Ccl1-Tfb3 from Saccharomyces cerevisiae. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: the yeast Cdk7 complex, that phosphorylates the RNA pol II C-terminal domain (CTD) in transcription initiation.
Cryogen name: ETHANE / Chamber humidity: 0 % / Chamber temperature: 293 K / Instrument: LEICA EM CPC Details: blotted for 2 seconds with Whatman 41 ashless filter paper.
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Electron microscopy
Microscope
FEI TITAN KRIOS
Specialist optics
Energy filter - Name: GIF Bioquantum
Image recording
Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4620 / Average exposure time: 2.24 sec. / Average electron dose: 45.0 e/Å2 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
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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