8S86

human PLD3 homodimer structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Lysosomal endonuclease RNase T2 and PLD exonucleases cooperatively generate RNA ligands for TLR7 activation.

Berouti, M.Lammens, K.Heiss, M.Hansbauer, L.Bauernfried, S.Stockl, J.Pinci, F.Piseddu, I.Greulich, W.Wang, M.Jung, C.Frohlich, T.Carell, T.Hopfner, K.P.Hornung, V.

(2024) Immunity 57: 1482

  • DOI: https://doi.org/10.1016/j.immuni.2024.04.010
  • Primary Citation of Related Structures:  
    8S86

  • PubMed Abstract: 

    Toll-like receptor 7 (TLR7) is essential for recognition of RNA viruses and initiation of antiviral immunity. TLR7 contains two ligand-binding pockets that recognize different RNA degradation products: pocket 1 recognizes guanosine, while pocket 2 coordinates pyrimidine-rich RNA fragments. We found that the endonuclease RNase T2, along with 5' exonucleases PLD3 and PLD4, collaboratively generate the ligands for TLR7. Specifically, RNase T2 generated guanosine 2',3'-cyclic monophosphate-terminated RNA fragments. PLD exonuclease activity further released the terminal 2',3'-cyclic guanosine monophosphate (2',3'-cGMP) to engage pocket 1 and was also needed to generate RNA fragments for pocket 2. Loss-of-function studies in cell lines and primary cells confirmed the critical requirement for PLD activity. Biochemical and structural studies showed that PLD enzymes form homodimers with two ligand-binding sites important for activity. Previously identified disease-associated PLD mutants failed to form stable dimers. Together, our data provide a mechanistic basis for the detection of RNA fragments by TLR7.


  • Organizational Affiliation

    Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-3' exonuclease PLD3
A, B
431Homo sapiensMutation(s): 0 
Gene Names: PLD3
EC: 3.1.16.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IV08 (Homo sapiens)
Explore Q8IV08 
Go to UniProtKB:  Q8IV08
PHAROS:  Q8IV08
GTEx:  ENSG00000105223 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IV08
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2024-05-15 
  • Deposition Author(s): Lammens, K.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection, Database references