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- EMDB-57794: PLD-fold vaccinia virus endonuclease K4 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-57794
TitlePLD-fold vaccinia virus endonuclease K4
Map dataOctamer of endonuclease K4
Sample
  • Complex: Octameric complex of K4
    • Protein or peptide: Virion nicking-joining enzyme
KeywordsNuclease / PLD / Phospholipase D / vaccinia virus / poxvirus / DNase / VIRAL PROTEIN
Function / homology
Function and homology information


virion component / endonuclease activity / hydrolase activity
Similarity search - Function
Phospholipase D / PLD-like domain / PLD3/4, PLD-like domain / : / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile.
Similarity search - Domain/homology
Virion nicking-joining enzyme
Similarity search - Component
Biological speciesVaccinia virus Copenhagen / Orthopoxvirus vaccinia
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsGroger H / Burmeister WP / Tarbouriech N
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0007-01 France
CitationJournal: J Mol Biol / Year: 2026
Title: High-resolution Structure of the Vaccinia Virus Phospholipase D-fold Endonuclease K4.
Authors: Henri Gröger / Candice Trouba / Jade Barbaste / Guillaume Lacroix / Guy Schoehn / Wim P Burmeister / Nicolas Tarbouriech /
Abstract: Vaccinia virus (VACV) is an orthopoxvirus closely related to mpox virus, which started global outbreaks in 2022. Poxvirus genomes are flanked by short, inverted complementary hairpin telomeres that ...Vaccinia virus (VACV) is an orthopoxvirus closely related to mpox virus, which started global outbreaks in 2022. Poxvirus genomes are flanked by short, inverted complementary hairpin telomeres that feature mismatched bases and insertions essential for viral replication. In this context, a role of the late protein K4 has been proposed. K4 is present in the virion, is apparently non-essential and has a phospholipase D (PLD)-fold as has VACV F13 protein. It also shares fold and nuclease activity with its closest homologue, mammalian PLD3. We established an endonuclease activity against ssDNA and hairpin loops and bubbles in a dsDNA context while RNA is resistant to cleavage. The 2.4 Å cryo-EM structure of K4 shows an unusual octameric assembly, also present in solution. At low concentration, tetramers and dimers similar to the one of hPLD3 are also present. Despite its nuclease activity, in K4 a C-terminal extension blocks the DNA binding pockets. Using an inactive mutant, fortuitously, a DNA 19mer bound simultaneously to 2 sites of the octamer where it displaced the C-termini. DNA binding uses similar residues as the hPLD3 5'-exonuclease, despite different activities and orientations of the DNA. The role of K4 and the control of its activity by the observed auto-inhibition remain enigmatic.
History
DepositionApr 28, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57794.png

Downloads & links

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Map

FileDownload / File: emd_57794.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOctamer of endonuclease K4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 256 pix.
= 293.12 Å		1.15 Å/pix.
x 256 pix.
= 293.12 Å		1.15 Å/pix.
x 256 pix.
= 293.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.145 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.13603923 - 0.3273021
Average (Standard dev.)0.0000743857 (±0.0113702165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 293.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Octamer of endonuclease K4 half map B

Fileemd_57794_half_map_1.map
AnnotationOctamer of endonuclease K4 half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Octamer of endonuclease K4 half map A

Fileemd_57794_half_map_2.map
AnnotationOctamer of endonuclease K4 half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Octameric complex of K4

EntireName: Octameric complex of K4
Components
  • Complex: Octameric complex of K4
    • Protein or peptide: Virion nicking-joining enzyme

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Supramolecule #1: Octameric complex of K4

SupramoleculeName: Octameric complex of K4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vaccinia virus Copenhagen
Molecular weightTheoretical: 392.61 KDa

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Macromolecule #1: Virion nicking-joining enzyme

MacromoleculeName: Virion nicking-joining enzyme / type: protein_or_peptide / ID: 1
Details: RES 1-28 : EXPRESSION TAG Protein fused to N-terminal TEV-cleavable 6xHis-tag
Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia / Strain: Copenhagen
Molecular weightTheoretical: 52.099266 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGAMANPD NTIAVITETI PIGMQFDKVY LSTFNMWREI LSNTTKTLDI SSFYWSLSDE VGTNFGTII LNEIVQLPKR GVRVRVAVNK SNKPLKDVER LQMAGVEVRY IDITNILGGV LHTKFWISDN THIYLGSANM D WRSLTQVK ...String:
MSYYHHHHHH DYDIPTTENL YFQGAMANPD NTIAVITETI PIGMQFDKVY LSTFNMWREI LSNTTKTLDI SSFYWSLSDE VGTNFGTII LNEIVQLPKR GVRVRVAVNK SNKPLKDVER LQMAGVEVRY IDITNILGGV LHTKFWISDN THIYLGSANM D WRSLTQVK ELGIAIFNNR NLAADLTQIF EVYWYLGVNN LPYNWKNFYP SYYNTDHPLS INVSGVPHSV FIASAPQQLC TM ERTNDLT ALLSCIRNAS KFVYVSVMNF IPIIYSKAGK ILFWPYIEDE LRRSAIDRQV SVKLLISCWQ RSSFIMRNFL RSI AMLKSK NIDIEVKLFI VPDADPPIPY SRVNHAKYMV TDKTAYIGTS NWTGNYFTDT CGASINITPD DGLGLRQQLE DIFM RDWNS KYSYELYDTS PTKRCKLLKN MKQCTNDIYC DEIQPEKEIP EYSLE

UniProtKB: Virion nicking-joining enzyme

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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

Concentration1 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl (pH 8), 150 mM NaCl, 2 mM DTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR / Details: EMS instruments
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3387 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 754920
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 97.1 / Target criteria: cross-correlation coefficient
Output model

PDB-30ie:
PLD-fold vaccinia virus endonuclease K4

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