8SP7

LINE-1 retrotransposon endonuclease domain complex with tranexamic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Identification and characterization of small molecule inhibitors of the LINE-1 retrotransposon endonuclease.

D'Ordine, A.M.Jogl, G.Sedivy, J.M.

(2024) Nat Commun 15: 3883-3883

  • DOI: https://doi.org/10.1038/s41467-024-48066-x
  • Primary Citation of Related Structures:  
    8SP5, 8SP7

  • PubMed Abstract: 

    The long interspersed nuclear element-1 (LINE-1 or L1) retrotransposon is the only active autonomously replicating retrotransposon in the human genome. L1 harms the cell by inserting new copies, generating DNA damage, and triggering inflammation. Therefore, L1 inhibition could be used to treat many diseases associated with these processes. Previous research has focused on inhibition of the L1 reverse transcriptase due to the prevalence of well-characterized inhibitors of related viral enzymes. Here we present the L1 endonuclease as another target for reducing L1 activity. We characterize structurally diverse small molecule endonuclease inhibitors using computational, biochemical, and biophysical methods. We also show that these inhibitors reduce L1 retrotransposition, L1-induced DNA damage, and inflammation reinforced by L1 in senescent cells. These inhibitors could be used for further pharmacological development and as tools to better understand the life cycle of this element and its impact on disease processes.


  • Organizational Affiliation

    Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LINE-1 retrotransposon endonuclease239Homo sapiensMutation(s): 0 
UniProt
Find proteins for V9H0D0 (Homo sapiens)
Explore V9H0D0 
Go to UniProtKB:  V9H0D0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9H0D0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMH (Subject of Investigation/LOI)
Query on AMH

Download Ideal Coordinates CCD File 
B [auth A]TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID
C8 H15 N O2
GYDJEQRTZSCIOI-LJGSYFOKSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.222α = 90
b = 64.671β = 90
c = 132.358γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_4895

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release