7DTH | pdb_00007dth

Solution structure of RPB6, common subunit of RNA polymerases I, II, and III


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Three human RNA polymerases interact with TFIIH via a common RPB6 subunit.

Okuda, M.Suwa, T.Suzuki, H.Yamaguchi, Y.Nishimura, Y.

(2022) Nucleic Acids Res 50: 1-16

  • DOI: https://doi.org/10.1093/nar/gkab612
  • Primary Citation Related Structures: 
    7DTH, 7DTI

  • PubMed Abstract: 

    In eukaryotes, three RNA polymerases (RNAPs) play essential roles in the synthesis of various types of RNA: namely, RNAPI for rRNA; RNAPII for mRNA and most snRNAs; and RNAPIII for tRNA and other small RNAs. All three RNAPs possess a short flexible tail derived from their common subunit RPB6. However, the function of this shared N-terminal tail (NTT) is not clear. Here we show that NTT interacts with the PH domain (PH-D) of the p62 subunit of the general transcription/repair factor TFIIH, and present the structures of RPB6 unbound and bound to PH-D by nuclear magnetic resonance (NMR). Using available cryo-EM structures, we modelled the activated elongation complex of RNAPII bound to TFIIH. We also provide evidence that the recruitment of TFIIH to transcription sites through the p62-RPB6 interaction is a common mechanism for transcription-coupled nucleotide excision repair (TC-NER) of RNAPI- and RNAPII-transcribed genes. Moreover, point mutations in the RPB6 NTT cause a significant reduction in transcription of RNAPI-, RNAPII- and RNAPIII-transcribed genes. These and other results show that the p62-RPB6 interaction plays multiple roles in transcription, TC-NER, and cell proliferation, suggesting that TFIIH is engaged in all RNAP systems.


  • Organizational Affiliation
    • Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

Macromolecule Content 

  • Total Structure Weight: 14.77 kDa 
  • Atom Count: 1,013 
  • Modeled Residue Count: 127 
  • Deposited Residue Count: 130 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2130Homo sapiensMutation(s): 0 
Gene Names: POLR2FPOLRF
UniProt & NIH Common Fund Data Resources
Find proteins for P61218 (Homo sapiens)
Explore P61218 
Go to UniProtKB:  P61218
PHAROS:  P61218
GTEx:  ENSG00000100142 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61218
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Other
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references