9ER2

PolII-TCR-STK19 structure.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair.

van den Heuvel, D.Rodriguez-Martinez, M.van der Meer, P.J.Nieto Moreno, N.Park, J.Kim, H.S.van Schie, J.J.M.Wondergem, A.P.D'Souza, A.Yakoub, G.Herlihy, A.E.Kashyap, K.Boissiere, T.Walker, J.Mitter, R.Apelt, K.de Lint, K.Kirdok, I.Ljungman, M.Wolthuis, R.M.F.Cramer, P.Scharer, O.D.Kokic, G.Svejstrup, J.Q.Luijsterburg, M.S.

(2024) Cell 187: 7107

  • DOI: https://doi.org/10.1016/j.cell.2024.10.018
  • Primary Citation of Related Structures:  
    9ER2

  • PubMed Abstract: 

    Transcription-coupled DNA repair (TCR) removes bulky DNA lesions impeding RNA polymerase II (RNAPII) transcription. Recent studies have outlined the stepwise assembly of TCR factors CSB, CSA, UVSSA, and transcription factor IIH (TFIIH) around lesion-stalled RNAPII. However, the mechanism and factors required for the transition to downstream repair steps, including RNAPII removal to provide repair proteins access to the DNA lesion, remain unclear. Here, we identify STK19 as a TCR factor facilitating this transition. Loss of STK19 does not impact initial TCR complex assembly or RNAPII ubiquitylation but delays lesion-stalled RNAPII clearance, thereby interfering with the downstream repair reaction. Cryoelectron microscopy (cryo-EM) and mutational analysis reveal that STK19 associates with the TCR complex, positioning itself between RNAPII, UVSSA, and CSA. The structural insights and molecular modeling suggest that STK19 positions the ATPase subunits of TFIIH onto DNA in front of RNAPII. Together, these findings provide new insights into the factors and mechanisms required for TCR.


  • Organizational Affiliation

    Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 1 of Inactive serine/threonine-protein kinase 19B [auth Q]258Homo sapiensMutation(s): 0 
Gene Names: STK19G11RP1
UniProt & NIH Common Fund Data Resources
Find proteins for P49842 (Homo sapiens)
Explore P49842 
Go to UniProtKB:  P49842
PHAROS:  P49842
GTEx:  ENSG00000204344 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49842
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitC [auth A]1,984Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A7M4DUC2 (Sus scrofa)
Explore A0A7M4DUC2 
Go to UniProtKB:  A0A7M4DUC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7M4DUC2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaD [auth B]1,167Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
Explore I3LGP4 
Go to UniProtKB:  I3LGP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LGP4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3E [auth C]275Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LCH3 (Sus scrofa)
Explore I3LCH3 
Go to UniProtKB:  I3LCH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LCH3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit DF [auth D]142Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287ADR4 (Sus scrofa)
Explore A0A287ADR4 
Go to UniProtKB:  A0A287ADR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A287ADR4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EG [auth E]210Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LSI7 (Sus scrofa)
Explore I3LSI7 
Go to UniProtKB:  I3LSI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LSI7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2H [auth F]127Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa)
Explore A0A4X1VEK9 
Go to UniProtKB:  A0A4X1VEK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1VEK9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitI [auth G]172Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VKG7 (Sus scrofa)
Explore A0A4X1VKG7 
Go to UniProtKB:  A0A4X1VKG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1VKG7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3J [auth H]150Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LCB2 (Sus scrofa)
Explore I3LCB2 
Go to UniProtKB:  I3LCB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LCB2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9K [auth I]125Sus scrofaMutation(s): 0 
UniProt
Find proteins for P60899 (Sus scrofa)
Explore P60899 
Go to UniProtKB:  P60899
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60899
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5L [auth J]67Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8W4F9W9 (Sus scrofa)
Explore A0A8W4F9W9 
Go to UniProtKB:  A0A8W4F9W9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8W4F9W9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-aM [auth K]117Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RKE4 (Sus scrofa)
Explore F1RKE4 
Go to UniProtKB:  F1RKE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1RKE4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit KN [auth L]58Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa)
Explore A0A4X1TRS6 
Go to UniProtKB:  A0A4X1TRS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1TRS6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
UV-stimulated scaffold protein AQ [auth c],
R [auth M]
709Homo sapiensMutation(s): 0 
Gene Names: UVSSAKIAA1530
UniProt & NIH Common Fund Data Resources
Find proteins for Q2YD98 (Homo sapiens)
Explore Q2YD98 
Go to UniProtKB:  Q2YD98
PHAROS:  Q2YD98
GTEx:  ENSG00000163945 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2YD98
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor 1 homologS [auth O]64Homo sapiensMutation(s): 0 
Gene Names: ELOF1
UniProt & NIH Common Fund Data Resources
Find proteins for P60002 (Homo sapiens)
Explore P60002 
Go to UniProtKB:  P60002
PHAROS:  P60002
GTEx:  ENSG00000130165 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60002
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-6T [auth b]1,493Homo sapiensMutation(s): 0 
Gene Names: ERCC6CSB
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q03468 (Homo sapiens)
Explore Q03468 
Go to UniProtKB:  Q03468
PHAROS:  Q03468
GTEx:  ENSG00000225830 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03468
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-8U [auth a]396Homo sapiensMutation(s): 0 
Gene Names: ERCC8CKN1CSA
UniProt & NIH Common Fund Data Resources
Find proteins for Q13216 (Homo sapiens)
Explore Q13216 
Go to UniProtKB:  Q13216
PHAROS:  Q13216
GTEx:  ENSG00000049167 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13216
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1V [auth d]1,140Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
IA [auth b]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF
Query on BEF

Download Ideal Coordinates CCD File 
JA [auth b]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth I]
CA [auth I]
DA [auth J]
EA [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
KA [auth b],
Y [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2024-12-04 
  • Deposition Author(s): Kokic, G.

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyEXC 2067/1-390729940
European Research Council (ERC)European UnionAdvanced Investigator Grant CHROMATRANS (grant agreement No. 882357)

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Data collection, Database references