8U3S | pdb_00008u3s

Structure of human TIRR in complex with VHH4 nanobody

  • Classification: RNA BINDING PROTEIN
  • Organism(s): Homo sapiens, Lama glama
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-09-08 Released: 2024-09-04 
  • Deposition Author(s): Botuyan, M.V., Mer, G.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.271 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

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


This is version 1.1 of the entry. See complete history


Literature

NEAT1 modulates the TIRR/53BP1 complex to maintain genome integrity.

Kilgas, S.Syed, A.Toolan-Kerr, P.Swift, M.L.Roychoudhury, S.Sarkar, A.Wilkins, S.Quigley, M.Poetsch, A.R.Botuyan, M.V.Cui, G.Mer, G.Ule, J.Drane, P.Chowdhury, D.

(2024) Nat Commun 15: 8438-8438

  • DOI: https://doi.org/10.1038/s41467-024-52862-w
  • Primary Citation of Related Structures:  
    8U3S

  • PubMed Abstract: 

    Tudor Interacting Repair Regulator (TIRR) is an RNA-binding protein (RBP) that interacts directly with 53BP1, restricting its access to DNA double-strand breaks (DSBs) and its association with p53. We utilized iCLIP to identify RNAs that directly bind to TIRR within cells, identifying the long non-coding RNA NEAT1 as the primary RNA partner. The high affinity of TIRR for NEAT1 is due to prevalent G-rich motifs in the short isoform (NEAT1_1) region of NEAT1. This interaction destabilizes the TIRR/53BP1 complex, promoting 53BP1's function. NEAT1_1 is enriched during the G1 phase of the cell cycle, thereby ensuring that TIRR-dependent inhibition of 53BP1's function is cell cycle-dependent. TDP-43, an RBP that is implicated in neurodegenerative diseases, modulates the TIRR/53BP1 complex by promoting the production of the NEAT1 short isoform, NEAT1_1. Together, we infer that NEAT1_1, and factors regulating NEAT1_1, may impact 53BP1-dependent DNA repair processes, with implications for a spectrum of diseases.


  • Organizational Affiliation
    • Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tudor-interacting repair regulator protein207Homo sapiensMutation(s): 0 
Gene Names: NUDT16L1SDOSTIRR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRJ7 (Homo sapiens)
Explore Q9BRJ7 
Go to UniProtKB:  Q9BRJ7
GTEx:  ENSG00000168101 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BRJ7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody125Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.271 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.076α = 90
b = 48.076β = 90
c = 238.906γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM136262
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA132878

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references, Structure summary