9VBI | pdb_00009vbi

Cryo-EM structure of PLD3 bound to ssDNA (poly(A))

• PDB DOI: https://doi.org/10.2210/pdb9VBI/pdb
• EM Map EMD-64923: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2025-06-04 Released: 2025-12-24 
• Deposition Author(s): Hirano, Y., Ezaki, W., Ohto, U., Shimizu, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanistic insights into single-stranded DNA degradation by lysosomal exonucleases PLD3 and PLD4 from structural snapshots.

Hirano, Y., Ezaki, W., Sato, R., Ohto, U., Miyake, K., Shimizu, T.

(2025) Nat Commun 

• PubMed: 41381514 
• DOI: https://doi.org/10.1038/s41467-025-66261-2
• Primary Citation of Related Structures:  
  9VBG, 9VBH, 9VBI, 9VBJ, 9VBK


• PubMed Abstract: 
  

  Lysosomal exonuclease phospholipase D (PLD) family PLD3 and PLD4 degrade single-stranded RNA or DNA and regulate TLR7 or TLR9 responses. Polymorphisms of these enzymes are associated with human diseases: PLD4 is associated with inflammatory diseases, and PLD3 is associated with neurodegenerative diseases. Here, we determine the structures of substrate-bound PLD3 and PLD4 by cryo-electron microscopy. Our structures reveal that PLD3 rebuilds a substrate-binding pocket, depending on the substrate, mainly via motion of the Phe335-containing loop. Furthermore, we captured the structure in a metastable state that appears during substrate rearrangement following product release. Together, our findings identify the residues that underlie the distinct activities of PLD3 and PLD4. This study provides a mechanistic basis for the exonuclease activity of PLD3 and PLD4 in single-stranded DNA degradation.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Synergy Institute for Futuristic Mucosal Vaccine Research and Development, Chiba University, Chiba, Japan.
Medical Mycology Research Center, Chiba University, Chiba, Japan.
Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 132.23 kDa 
• Atom Count: 7,066 
• Modeled Residue Count: 850 
• Deposited Residue Count: 970 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-3' exonuclease PLD3	B [auth A], D	436	Homo sapiens	Mutation(s): 2  Gene Names: PLD3 EC: 3.1.16.1 (PDB Primary Data), 3.1.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IV08 (Homo sapiens) Explore Q8IV08  Go to UniProtKB:  Q8IV08
PHAROS:  Q8IV08 GTEx:  ENSG00000105223
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: Q8IV08-1

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*AP*A)-3')	A [auth C], C [auth B]	49	synthetic construct

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H, I, L	2		N-Glycosylation

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, J	3		N-Glycosylation

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, K	5		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Hirano, Y., Ezaki, W., Ohto, U., Shimizu, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22K06110
Japan Society for the Promotion of Science (JSPS)	Japan	25K09523
Japan Science and Technology	Japan	JPMJCR21E4

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release