9QPX | pdb_00009qpx

BRCA1 BRCT tandem repeat with RNA polymerase II pSer5-CTD peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.312 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.265 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9QPX

This is version 1.0 of the entry. See complete history

Literature

Distinct mechanisms of recognition of phosphorylated RNAPII C-terminal domain by BRCT repeats of the BRCA1-BARD1 complex.

Klapstova, V.Sedova, K.Houser, J.Sebesta, M.

(2025) J Biological Chem 302: 111010-111010

  • DOI: https://doi.org/10.1016/j.jbc.2025.111010
  • Primary Citation Related Structures: 
    9QPX

  • PubMed Abstract: 

    Transcription competes with other DNA-dependent processes, such as DNA repair, for access to its substrate, DNA. However, the principles governing the interplay between these processes remain poorly understood. Evidence suggests that the BRCA1-BARD1 complex, a key player in the DNA damage response, may act as a mediator of this crosstalk. In this study, we investigated the molecular mechanism underpinning the interaction between RNA polymerase II (RNAPII) and the BRCA1-BARD1 complex, as well as its functional implications. Our findings reveal that the tandem BRCT domain of BRCA1 binds the Ser5-phosphorylated CTD of RNAPII, utilizing a mechanism previously established for other BRCA1 BRCT ligands. Furthermore, we demonstrate that this interaction is critical for the organization of RNAPII into condensates with liquid-like properties. Analysis of disease-associated variants within the BRCT repeats further supports the biological relevance of this condensation. Collectively, our results suggest that the BRCA1-BARD1 complex may coordinate transcription and DNA repair by facilitating the organization of RNAPII into transcription factories.


  • Organizational Affiliation
    • CEITEC-Central European Institute of Technology, Masaryk University Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University Brno, Czechia.

Macromolecule Content 

  • Total Structure Weight: 103.26 kDa 
  • Atom Count: 6,819 
  • Modeled Residue Count: 872 
  • Deposited Residue Count: 902 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Breast cancer type 1 susceptibility proteinA,
B [auth D],
C [auth B],
D [auth C]
215Homo sapiensMutation(s): 0 
Gene Names: BRCA1RNF53
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P38398 (Homo sapiens)
Explore P38398 
Go to UniProtKB:  P38398
PHAROS:  P38398
GTEx:  ENSG00000012048 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38398
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1E [auth F],
F [auth E],
G
14Homo sapiensMutation(s): 0 
EC: 2.7.7.6 (PDB Primary Data), 3.1.13 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P24928 (Homo sapiens)
Explore P24928 
Go to UniProtKB:  P24928
PHAROS:  P24928
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24928
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
E [auth F],
F [auth E],
G
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.312 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.265 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.827α = 90
b = 134.762β = 90
c = 180.381γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant Agency of the Czech RepublicCzech Republic21-10464M
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2023050
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2023042
European Regional Development FundEuropean UnionCZ.02.01.01/00/23_015/0008175

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-14
    Type: Initial release