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- EMDB-58870: Bacterial antiviral defense protein PD-T7-3 (82-84 residues delet... -

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Basic information

Entry
Database: EMDB / ID: EMD-58870
TitleBacterial antiviral defense protein PD-T7-3 (82-84 residues deleted) obtained from a sample containing single-stranded DNA and tRNA
Map dataUnsharpened map
Sample
  • Complex: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, 82-84 residues deleted.
    • Protein or peptide: Bacterial antiviral defense protein PD-T7-3
KeywordsHEPN domain / nuclease / bacterial antiviral protein / PD-T7-3 / ANTIVIRAL PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsPuteikiene R / Sasnauskas G
Funding supportLithuania, 1 items
OrganizationGrant numberCountry
Research Council of LithuaniaS-MIP-22-13Lithuania
CitationJournal: To Be Published
Title: Viral SSB-bound ssDNA activates the bacterial anti-phage defense system DARNA
Authors: Puteikiene R / Vassallo CN / Silanskas A / Songailiene I / Juozapaitis J / Laub MT / Sasnauskas G
History
DepositionJul 8, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58870.png

Downloads & links

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Map

FileDownload / File: emd_58870.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.18542914 - 0.50304544
Average (Standard dev.)-0.001972932 (±0.011080612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58870_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_58870_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_58870_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Bacterial antiviral defense protein PD-T7-3 from Escherichia coli...

EntireName: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, 82-84 residues deleted.
Components
  • Complex: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, 82-84 residues deleted.
    • Protein or peptide: Bacterial antiviral defense protein PD-T7-3

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Supramolecule #1: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli...

SupramoleculeName: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, 82-84 residues deleted.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Obtained from a sample containing ssDNA and tRNA.
Source (natural)Organism: Escherichia coli (E. coli) / Strain: ECOR30

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Macromolecule #1: Bacterial antiviral defense protein PD-T7-3

MacromoleculeName: Bacterial antiviral defense protein PD-T7-3 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: ECOR30
Molecular weightTheoretical: 54.291645 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDVRIFSLES QKSKIYDRRT RKYFEEVYKS YANGCYRSAT VMLWSVVVCD IIFKLQELRD VHNDAVAEKI LLEIEALQND DPKWEKELI KRVFERTQLL DTASNHKVLL IQKHRHLSAH PVISDEDTLF EPTQEMIRSD IRNSIEVILS KPPFMSQKIL S TFVADLEK ...String:
MDVRIFSLES QKSKIYDRRT RKYFEEVYKS YANGCYRSAT VMLWSVVVCD IIFKLQELRD VHNDAVAEKI LLEIEALQND DPKWEKELI KRVFERTQLL DTASNHKVLL IQKHRHLSAH PVISDEDTLF EPTQEMIRSD IRNSIEVILS KPPFMSQKIL S TFVADLEK VKDLFPSDNA LKKYLDVKYF KSLNKEVLVK IFKGLWKFSF RSEEAKPLEN REINIRAMKL IFEKDRQAMV DS VKAETAY YSNISNNHDA IKALIEFISM EKEIYNALDD SVKELIKPII KDNISYFGIA FFISESPEEH INRVTKRISE KYY KKYGDN GNFLNQQHLA IFKNVCSELG LESEYRDFGI ACFINSADFE RADIYFDRFI DKDLANYSSE QMLTLLEGAN KNNQ CYWRN RSRNGNDSIR ILKAAKNKLP DGFDFSKYDN LPVDKIDHVL EEDVGERFES GHHHHHH

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
SoftwareName: EPU (ver. 3.13)
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2811 / Average electron dose: 29.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 92000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC ab-initio model
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 92684
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-32ge:
Bacterial antiviral defense protein PD-T7-3 (82-84 residues deleted) obtained from a sample containing single-stranded DNA and tRNA

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