9BZ0 | pdb_00009bz0

Structure of an STK19-containing TC-NER complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

STK19 positions TFIIH for cell-free transcription-coupled DNA repair.

Mevissen, T.E.T.Kummecke, M.Schmid, E.W.Farnung, L.Walter, J.C.

(2024) Cell 187: 7091-7106.e24

  • DOI: https://doi.org/10.1016/j.cell.2024.10.020
  • Primary Citation Related Structures: 
    9BZ0

  • PubMed Abstract: 

    In transcription-coupled nucleotide excision repair (TC-NER), stalled RNA polymerase II (RNA Pol II) binds CSB and CRL4 CSA , which cooperate with UVSSA and ELOF1 to recruit TFIIH. To explore the mechanism of TC-NER, we recapitulated this reaction in vitro. When a plasmid containing a site-specific lesion is transcribed in frog egg extract, error-free repair is observed that depends on CSB, CRL4 CSA , UVSSA, and ELOF1. Repair also requires STK19, a factor previously implicated in transcription recovery after UV exposure. A 1.9-Å cryo-electron microscopy structure shows that STK19 binds the TC-NER complex through CSA and the RPB1 subunit of RNA Pol II. Furthermore, AlphaFold predicts that STK19 interacts with the XPD subunit of TFIIH, and disrupting this interface impairs cell-free repair. Molecular modeling suggests that STK19 positions TFIIH ahead of RNA Pol II for lesion verification. Our analysis of cell-free TC-NER suggests that STK19 couples RNA Pol II stalling to downstream repair events.


  • Organizational Affiliation
    • Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 1,058.1 kDa 
  • Atom Count: 54,687 
  • Modeled Residue Count: 6,730 
  • Deposited Residue Count: 9,059 
  • Unique protein chains: 19
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit1,984Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A7M4DUC2 (Sus scrofa)
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UniProt GroupA0A7M4DUC2
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,251Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A0B8RVL1 (Sus scrofa domesticus)
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UniProt GroupA0A0B8RVL1
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3275Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LCH3 (Sus scrofa)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA polymerase Rpb4/RPC9 core domain-containing protein142Sus scrofaMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit E210Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LSI7 (Sus scrofa)
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UniProt GroupI3LSI7
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2127Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa)
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UniProt GroupA0A4X1VEK9
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7172Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA0A4X1VKG7
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Sus scrofaMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Sus scrofaMutation(s): 0 
UniProt
Find proteins for P60899 (Sus scrofa)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8W4F9W9 (Sus scrofa)
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UniProt GroupA0A8W4F9W9
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA polymerase II subunit J117Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0TE17 (Sus scrofa)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA polymerase II subunit K58Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription elongation factor 1 homolog85Homo sapiensMutation(s): 0 
UniProt
Find proteins for A0A2K5RSX0 (Cebus imitator)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-8Q [auth a]396Homo sapiensMutation(s): 0 
Gene Names: ERCC8CKN1CSA
UniProt & NIH Common Fund Data Resources
Find proteins for Q13216 (Homo sapiens)
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PHAROS:  Q13216
GTEx:  ENSG00000049167 
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-6R [auth b]1,496Homo sapiensMutation(s): 2 
Gene Names: ERCC6CSB
EC: 3.6.4
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Find proteins for Q03468 (Homo sapiens)
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PHAROS:  Q03468
GTEx:  ENSG00000225830 
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
UV-stimulated scaffold protein AS [auth c]712Homo sapiensMutation(s): 0 
Gene Names: UVSSAKIAA1530
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Find proteins for Q2YD98 (Homo sapiens)
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PHAROS:  Q2YD98
GTEx:  ENSG00000163945 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1T [auth d]1,143Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
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Find proteins for Q16531 (Homo sapiens)
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PHAROS:  Q16531
GTEx:  ENSG00000167986 
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
DET1- and DDB1-associated protein 1U [auth e]105Homo sapiensMutation(s): 0 
Gene Names: DDA1C19orf58PCIA1
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Find proteins for Q9BW61 (Homo sapiens)
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PHAROS:  Q9BW61
GTEx:  ENSG00000130311 
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Inactive serine/threonine-protein kinase 19V [auth f]254Homo sapiensMutation(s): 0 
Gene Names: STK19G11RP1
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Find proteins for P49842 (Homo sapiens)
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PHAROS:  P49842
GTEx:  ENSG00000204344 
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UniProt GroupP49842
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Reference Sequence
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (35-MER)90synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3')O [auth P]10synthetic construct
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Reference Sequence
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Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (49-MER)P [auth T]90synthetic construct
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth I]
CA [auth I]
DA [auth J]
EA [auth L]
AA [auth C],
BA [auth I],
CA [auth I],
DA [auth J],
EA [auth L],
FA [auth M],
HA [auth c],
W [auth A],
X [auth A],
Z [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
GA [auth b],
Y [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesDP2-ES036404
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesHL098316

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Data collection, Database references