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- EMDB-64921: Cryo-EM structure of human PLD3 apo form -

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Basic information

Entry
Database: EMDB / ID: EMD-64921
TitleCryo-EM structure of human PLD3 apo form
Map data
Sample
  • Complex: Homodimer of PLD3 luminal domain
    • Protein or peptide: 5'-3' exonuclease PLD3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsExonuclease / IMMUNE SYSTEM
Function / homology
Function and homology information


spleen exonuclease / Synthesis of PG / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / D-type glycerophospholipase activity / regulation of cytokine production involved in inflammatory response / immune system process / Role of phospholipids in phagocytosis / lysosomal lumen ...spleen exonuclease / Synthesis of PG / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / D-type glycerophospholipase activity / regulation of cytokine production involved in inflammatory response / immune system process / Role of phospholipids in phagocytosis / lysosomal lumen / lipid metabolic process / late endosome membrane / early endosome membrane / inflammatory response / Golgi membrane / lysosomal membrane / endoplasmic reticulum membrane / extracellular exosome
Similarity search - Function
PLD-like domain / PLD-like domain / : / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile.
Similarity search - Domain/homology
5'-3' exonuclease PLD3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsHirano Y / Ezaki W / Ohto U / Shimizu T
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K06110 Japan
Japan Society for the Promotion of Science (JSPS)25K09523 Japan
Japan Science and TechnologyJPMJCR21E4 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Mechanistic insights into single-stranded DNA degradation by lysosomal exonucleases PLD3 and PLD4 from structural snapshots.
Authors: Yoshinori Hirano / Wakiko Ezaki / Ryota Sato / Umeharu Ohto / Kensuke Miyake / Toshiyuki Shimizu /
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 ...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.
History
DepositionJun 4, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64921.png

Downloads & links

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Map

FileDownload / File: emd_64921.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.056648318 - 0.1442121
Average (Standard dev.)0.00014777445 (±0.0035224827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64921_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64921_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Homodimer of PLD3 luminal domain

EntireName: Homodimer of PLD3 luminal domain
Components
  • Complex: Homodimer of PLD3 luminal domain
    • Protein or peptide: 5'-3' exonuclease PLD3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Homodimer of PLD3 luminal domain

SupramoleculeName: Homodimer of PLD3 luminal domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 5'-3' exonuclease PLD3

MacromoleculeName: 5'-3' exonuclease PLD3 / type: protein_or_peptide / ID: 1
Details: C-terminal 6 residues (LEVLFQ) are derived from the expression tag.
Number of copies: 2 / Enantiomer: LEVO / EC number: spleen exonuclease
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.601664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EYGDLHLFGP NQRPAPCYDP CEAVLVESIP EGLDFPNAST GNPSTSQAWL GLLAGAHSSL DIASFYWTLT NNDTHTQEPS AQQGEEVLR QLQTLAPKGV NVRIAVSKPS GPQPQADLQA LLQSGAQVRM VDMQKLTHGV LHTKFWVVDQ THFYLGSANM D WRSLTQVK ...String:
EYGDLHLFGP NQRPAPCYDP CEAVLVESIP EGLDFPNAST GNPSTSQAWL GLLAGAHSSL DIASFYWTLT NNDTHTQEPS AQQGEEVLR QLQTLAPKGV NVRIAVSKPS GPQPQADLQA LLQSGAQVRM VDMQKLTHGV LHTKFWVVDQ THFYLGSANM D WRSLTQVK ELGVVMYNCS CLARDLTKIF EAYWFLGQAG SSIPSTWPRF YDTRYNQETP MEICLNGTPA LAYLASAPPP LC PSGRTPD LKALLNVVDN ARSFIYVAVM NYLPTLEFSH PHRFWPAIDD GLRRATYERG VKVRLLISCW GHSEPSMRAF LLS LAALRD NHTHSDIQVK LFVVPADEAQ ARIPYARVNH NKYMVTERAT YIGTSNWSGN YFTETAGTSL LVTQNGRGGL RSQL EAIFL RDWDSPYSHD LDTSADSVGN ACRLLLEVLF Q

UniProtKB: 5'-3' exonuclease PLD3

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 503473
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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