7KIU

Structure of recombinant human DNase1L3 in complex with Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural features of Dnase1L3 responsible for serum antigen clearance.

McCord, J.J.Engavale, M.Masoumzadeh, E.Villarreal, J.Mapp, B.Latham, M.P.Keyel, P.A.Sutton, R.B.

(2022) Commun Biol 5: 825-825

  • DOI: https://doi.org/10.1038/s42003-022-03755-5
  • Primary Citation of Related Structures:  
    7KIU

  • PubMed Abstract: 

    Autoimmunity develops when extracellular DNA released from dying cells is not cleared from serum. While serum DNA is primarily digested by Dnase1 and Dnase1L3, Dnase1 cannot rescue autoimmunity arising from Dnase1L3 deficiencies. Dnase1L3 uniquely degrades antigenic forms of cell-free DNA, including DNA complexed with lipids and proteins. The distinct activity of Dnase1L3 relies on its unique C-terminal Domain (CTD), but the mechanism is unknown. We used multiple biophysical techniques and functional assays to study the interplay between the core catalytic domain and the CTD. While the core domain resembles Dnase1, there are key structural differences between the two enzymes. First, Dnase1L3 is not inhibited by actin due to multiple differences in the actin recognition site. Second, the CTD augments the ability of the core to bind DNA, thereby facilitating the degradation of complexed DNA. Together, these structural insights will inform the development of Dnase1L3-based therapies for autoimmunity.


  • Organizational Affiliation

    Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyribonuclease gamma
A, B, C, D
281Homo sapiensMutation(s): 0 
Gene Names: DNASE1L3DHP2DNAS1L3
EC: 3.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q13609 (Homo sapiens)
Explore Q13609 
Go to UniProtKB:  Q13609
PHAROS:  Q13609
GTEx:  ENSG00000163687 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13609
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth B]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth C],
L [auth C],
M [auth C],
N [auth D],
O [auth D],
P [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.313α = 85.394
b = 72.671β = 80.558
c = 73.169γ = 88.392
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
XDSdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description