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- EMDB-52475: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli... -

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Basic information

Entry
Database: EMDB / ID: EMD-52475
TitleBacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 saturated with pdCpdG dinucleotide (HEPN active site mutant R502A)
Map datasharpened map (phenix.auto_sharpen b_iso_to_d_cut, 2.43)
Sample
  • Complex: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 saturated with pdCpdG dinucleotide (HEPN active site mutant R502A)
    • Protein or peptide: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
    • DNA: DNA (5'-D(P*CP*G)-3')
  • Ligand: ZINC ION
KeywordsApeA / HEPN domain / bacterial antiviral defence / RNA BINDING PROTEIN
Biological speciesEscherichia coli 2-156-04_S4_C1 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.43 Å
AuthorsSasnauskas G / Juozapaitis J / Puteikiene R / Tamulaitiene G
Funding supportLithuania, 1 items
OrganizationGrant numberCountry
Research Council of LithuaniaS-MIP-22-13Lithuania
CitationJournal: To Be Published
Title: ApeA is a deoxyribodinucleotide binding antiviral defense system targeting tRNA
Authors: Juozapaitis J / Silanskas A / Ruksenaite A / Puteikiene R / Truncaite L / Songailiene I / Tamulaitiene G / Siksnys V / Sasnauskas G
History
DepositionJan 7, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52475.png

Downloads & links

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Map

FileReleased
Annotationsharpened map (phenix.auto_sharpen b_iso_to_d_cut, 2.43)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. 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: 5.0
Minimum - Maximum-13.356603 - 36.751506999999997
Average (Standard dev.)0.000000000000169 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52475_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map, input to phenix.auto sharpen

Fileemd_52475_additional_1.map
Annotationunsharpened map, input to phenix.auto_sharpen
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_52475_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_52475_half_map_2.map
Annotationhalf map 1
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 Ec2ApeA from Escherichia coli...

EntireName: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 saturated with pdCpdG dinucleotide (HEPN active site mutant R502A)
Components
  • Complex: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 saturated with pdCpdG dinucleotide (HEPN active site mutant R502A)
    • Protein or peptide: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
    • DNA: DNA (5'-D(P*CP*G)-3')
  • Ligand: ZINC ION

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Supramolecule #1: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli...

SupramoleculeName: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 saturated with pdCpdG dinucleotide (HEPN active site mutant R502A)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli 2-156-04_S4_C1 (bacteria)

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Macromolecule #1: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli...

MacromoleculeName: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli 2-156-04_S4_C1 (bacteria)
Molecular weightTheoretical: 69.18793 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKFRRLHNWN HIEQCTALIY FTELMEELLF DYTHSTYKPS IMNTPSLCIE AISTIDDIEK GNISPAHISH VIDELTKNIK NDDIAISLL KNPLGSFLDQ LQNNQLGNKN LKITLELLRV QLNVGNYESK LISELCSTIT SEYNPNKIRK FTRLLITHLI S KGLSQEYL ...String:
MKFRRLHNWN HIEQCTALIY FTELMEELLF DYTHSTYKPS IMNTPSLCIE AISTIDDIEK GNISPAHISH VIDELTKNIK NDDIAISLL KNPLGSFLDQ LQNNQLGNKN LKITLELLRV QLNVGNYESK LISELCSTIT SEYNPNKIRK FTRLLITHLI S KGLSQEYL MESLKKHFFQ REREISSNEE IITFLENIPS ETQEYSVYFN AEKSFSYITP CLSQLEIEVV LETPENINET DF FDNHEQR TILVKHVKAL DPFTARRVAE RNLKLASTLL SLYHHKQEAS WSAENIVVSE NGEKINIRSS INPMHRCKDL VQE HASRRL EQFMNNFRMR KDSFNKFIRS VQLHSMALQT NAVENQLLNL WIAIESLIPD ESKKEEQSTI EHIVNSLTPF LNLN YIEDL VRNLIKDLQR WNHPRTMSLL RLIGDSDAAK SFVILVASQE HAPSINQFKI ELSQFPLLKE RFEYISNLIS STDTM YQAL KNHAERINWQ IRRIYRTANL IVHTGKTPSK TNVLVEHAHI YLDAVINSLI KLSSHPVEIL SVAQGFRNVE MKYKMY IQK LNKKNIELTP ENIISFIFNQ LESGHHHHHH

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Macromolecule #2: DNA (5'-D(P*CP*G)-3')

MacromoleculeName: DNA (5'-D(P*CP*G)-3') / type: dna / ID: 2 / Number of copies: 10 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 573.43 Da
SequenceString:
(DC)(DG)

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 10 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
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: 2040 / Average electron dose: 30.0 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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC ab-initio model
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 358680
Initial angle assignmentType: MAXIMUM LIKELIHOOD
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-9hxg:
Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 saturated with pdCpdG dinucleotide (HEPN active site mutant R502A)

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