6XI8 | pdb_00006xi8

Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6XI8

This is version 1.1 of the entry. See complete history

Literature

Structure of TFIIK for phosphorylation of CTD of RNA polymerase II.

van Eeuwen, T.Li, T.Kim, H.J.Gorbea Colon, J.J.Parker, M.I.Dunbrack, R.L.Garcia, B.A.Tsai, K.L.Murakami, K.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abd4420
  • Primary Citation Related Structures: 
    6XI8, 7KUE

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Macromolecule Content 

  • Total Structure Weight: 79.98 kDa 
  • Atom Count: 5,022 
  • Modeled Residue Count: 636 
  • Deposited Residue Count: 688 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA polymerase II transcription factor B subunit 3A [auth C]63Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q03290 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03290 
Go to UniProtKB:  Q03290
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03290
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase KIN28B [auth A]301Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.11.23
UniProt
Find proteins for P06242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06242 
Go to UniProtKB:  P06242
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06242
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclin CCL1C [auth B]324Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P37366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P37366 
Go to UniProtKB:  P37366
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37366
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
B [auth A]L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.8
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM123233

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references, Refinement description, Structure summary