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- EMDB-56172: Bacterial antiviral defense protein PD-T7-3 (H122A) in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-56172
TitleBacterial antiviral defense protein PD-T7-3 (H122A) in complex with single-stranded DNA and a fragment of RNA
Map datacomposite map
Sample
  • Complex: Bacterial antiviral defense protein PD-T7-3 (H122A) in complex with single-stranded DNA and a fragment of RNA
    • Protein or peptide: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
    • DNA: single-stranded DNA
    • RNA: RNA
    • RNA: RNA
KeywordsHEPN domain / nuclease / bacterial antiviral protein / PD-T7-3 / ANTIVIRAL PROTEIN
Biological speciesEscherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsPuteikiene R / Sasnauskas G
Funding supportLithuania, 1 items
OrganizationGrant numberCountry
Research Council of LithuaniaS-MIP-22-13Lithuania
CitationJournal: To Be Published
Title: Standalone anti-phage HEPN nuclease PD-T7-3 is activated by ssDNA for tRNA cleavage
Authors: Puteikiene R / Vassallo CN / Silanskas A / Songailiene I / Juozapaitis J / Laub MT / Sasnauskas G
History
DepositionDec 23, 2025-
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_56172.png

Downloads & links

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Map

FileDownload / File: emd_56172.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite 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: 0.09
Minimum - Maximum-0.12955901 - 0.7308875
Average (Standard dev.)-0.0003783771 (±0.014039868)
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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Additional map: sharpened composite map (phenix.auto sharpen b iso to d cut, 3.3)

Fileemd_56172_additional_1.map
Annotationsharpened composite map (phenix.auto_sharpen b_iso_to_d_cut, 3.3)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacterial antiviral defense protein PD-T7-3 (H122A) in complex wi...

EntireName: Bacterial antiviral defense protein PD-T7-3 (H122A) in complex with single-stranded DNA and a fragment of RNA
Components
  • Complex: Bacterial antiviral defense protein PD-T7-3 (H122A) in complex with single-stranded DNA and a fragment of RNA
    • Protein or peptide: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
    • DNA: single-stranded DNA
    • RNA: RNA
    • RNA: RNA

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Supramolecule #1: Bacterial antiviral defense protein PD-T7-3 (H122A) in complex wi...

SupramoleculeName: Bacterial antiviral defense protein PD-T7-3 (H122A) in complex with single-stranded DNA and a fragment of RNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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, HEPN active site mutant H122A
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: ECOR30
Molecular weightTheoretical: 54.571945 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDVRIFSLES QKSKIYDRRT RKYFEEVYKS YANGCYRSAT VMLWSVVVCD IIFKLQELRD VHNDAVAEKI LLEIEALQND DPYSPKWEK ELIKRVFERT QLLDTASNHK VLLIQKHRHL SAAPVISDED TLFEPTQEMI RSDIRNSIEV ILSKPPFMSQ K ILSTFVAD ...String:
MDVRIFSLES QKSKIYDRRT RKYFEEVYKS YANGCYRSAT VMLWSVVVCD IIFKLQELRD VHNDAVAEKI LLEIEALQND DPYSPKWEK ELIKRVFERT QLLDTASNHK VLLIQKHRHL SAAPVISDED 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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Macromolecule #2: single-stranded DNA

MacromoleculeName: single-stranded DNA / type: dna / ID: 2 / Number of copies: 4 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.358687 KDa
SequenceString:
(DA)(DC)(DG)(DG)(DC)(DC)(DT)(DT)(DC)(DA) (DA)(DT)(DT)(DA)(DT)(DA)(DG)(DT)(DT)(DC) (DC)(DT)(DA)(DT)(DT)(DA)(DA)(DA)(DT) (DT)(DC)(DT)(DC)(DG)

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Macromolecule #3: RNA

MacromoleculeName: RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.588689 KDa
SequenceString:
AAAAAAAA

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Macromolecule #4: RNA

MacromoleculeName: RNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.404369 KDa
SequenceString:
UUUUUUUU

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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
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2582 / 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1)
Details: Number of particles after D2 symmetry expansion. Resolution calculated as the mean resolution value of consensus map and two focus maps.
Number images used: 115980
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

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

PDB-9trd:
Bacterial antiviral defense protein PD-T7-3 (H122A) in complex with single-stranded DNA and a fragment of RNA

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