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- EMDB-58869: Bacterial antiviral defense protein PD-T7-3 obtained from a sampl... -

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Basic information

Entry
Database: EMDB / ID: EMD-58869
TitleBacterial antiviral defense protein PD-T7-3 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
    • Protein or peptide: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30
KeywordsHEPN domain / nuclease / bacterial antiviral protein / PD-T7-3 / ANTIVIRAL PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 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_58869.png

Downloads & links

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Map

FileDownload / File: emd_58869.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
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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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.16863789 - 0.47256634
Average (Standard dev.)-0.0027898757 (±0.0119632995)
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_58869_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_58869_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_58869_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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
Components
  • Complex: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30
    • Protein or peptide: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30

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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
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 from Escherichia coli...

MacromoleculeName: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: ECOR30
Molecular weightTheoretical: 54.639012 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDVRIFSLES QKSKIYDRRT RKYFEEVYKS YANGCYRSAT VMLWSVVVCD IIFKLQELRD VHNDAVAEKI LLEIEALQND DPYSPKWEK ELIKRVFERT QLLDTASNHK VLLIQKHRHL SAHPVISDED TLFEPTQEMI RSDIRNSIEV ILSKPPFMSQ K ILSTFVAD ...String:
MDVRIFSLES QKSKIYDRRT RKYFEEVYKS YANGCYRSAT VMLWSVVVCD IIFKLQELRD VHNDAVAEKI LLEIEALQND DPYSPKWEK ELIKRVFERT QLLDTASNHK VLLIQKHRHL SAHPVISDED TLFEPTQEMI RSDIRNSIEV ILSKPPFMSQ K ILSTFVAD LEKVKDLFPS DNALKKYLDV KYFKSLNKEV LVKIFKGLWK FSFRSEEAKP LENREINIRA MKLIFEKDRQ AM VDSVKAE TAYYSNISNN HDAIKALIEF ISMEKEIYNA LDDSVKELIK PIIKDNISYF GIAFFISESP EEHINRVTKR ISE KYYKKY GDNGNFLNQQ HLAIFKNVCS ELGLESEYRD FGIACFINSA DFERADIYFD RFIDKDLANY SSEQMLTLLE GANK NNQCY WRNRSRNGND SIRILKAAKN KLPDGFDFSK YDNLPVDKID HVLEEDVGER FESGHHHHHH

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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: 1491 / 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: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 128877
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-32gd:
Bacterial antiviral defense protein PD-T7-3 obtained from a sample containing single-stranded DNA and tRNA

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