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- EMDB-52481: Putative bacterial antiviral defense protein Thr1ApeA from Thermo... -

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Basic information

Entry
Database: EMDB / ID: EMD-52481
TitlePutative bacterial antiviral defense protein Thr1ApeA from Thermoactinospora rubra strain YIM 77501
Map datasharpened map (phenix.auto_sharpen b_iso_to_d_cut, 3.1)
Sample
  • Complex: Putative bacterial antiviral defense protein Thr1ApeA from Thermoactinospora rubra strain YIM 77501
    • Protein or peptide: Putative bacterial antiviral defense protein Thr1ApeA from Thermoactinospora rubra strain YIM 77501
KeywordsApeA / HEPN domain / bacterial antiviral defence / RNA BINDING PROTEIN
Biological speciesThermoactinospora rubra (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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_52481.png

Downloads & links

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Map

FileReleased
Annotationsharpened map (phenix.auto_sharpen b_iso_to_d_cut, 3.1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. 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-31.190325000000001 - 41.041428000000003
Average (Standard dev.)-0.000000000002186 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52481_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_52481_additional_1.map
Annotationunsharpened map, input to phenix.auto_sharpen
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: half map 1

Fileemd_52481_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_52481_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Putative bacterial antiviral defense protein Thr1ApeA from Thermo...

EntireName: Putative bacterial antiviral defense protein Thr1ApeA from Thermoactinospora rubra strain YIM 77501
Components
  • Complex: Putative bacterial antiviral defense protein Thr1ApeA from Thermoactinospora rubra strain YIM 77501
    • Protein or peptide: Putative bacterial antiviral defense protein Thr1ApeA from Thermoactinospora rubra strain YIM 77501

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Supramolecule #1: Putative bacterial antiviral defense protein Thr1ApeA from Thermo...

SupramoleculeName: Putative bacterial antiviral defense protein Thr1ApeA from Thermoactinospora rubra strain YIM 77501
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermoactinospora rubra (bacteria)

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Macromolecule #1: Putative bacterial antiviral defense protein Thr1ApeA from Thermo...

MacromoleculeName: Putative bacterial antiviral defense protein Thr1ApeA from Thermoactinospora rubra strain YIM 77501
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermoactinospora rubra (bacteria)
Molecular weightTheoretical: 60.696988 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTAGTPQTDA LVKARILELL ESWSPWHRRL WDLGTVLAMR EVIEAADWVG RHVLSRAALS WCVQESLLPR LKTDGAIGDG EVRRQLHQL CKSPIKPAAR SQRALGHLTD LVADGYLRRW RDLVATAPVH VERSARCITS HVLDSGFHQD FLRRHLRSRL D ESSTAVDV ...String:
MTAGTPQTDA LVKARILELL ESWSPWHRRL WDLGTVLAMR EVIEAADWVG RHVLSRAALS WCVQESLLPR LKTDGAIGDG EVRRQLHQL CKSPIKPAAR SQRALGHLTD LVADGYLRRW RDLVATAPVH VERSARCITS HVLDSGFHQD FLRRHLRSRL D ESSTAVDV IELFMELEEQ GEQTYEGMIV LQDKLPAAQV AIKSPIWLSQ EEVAHRLATG FPHVTGIRIS GGLLFRVRAR DH VSAVHEI TELFDRIRNR VRYRRGQTRL DVYPQVFLAG QPEPQEFVRG DPAVSVVSLE RVGLLYELPE TGTHGSRIDD ALE LAAALT ESSPSKAVAG AWAAIEALLF CDTDEADREE GRAVAADRAA ALVAAGWPRA ELTTLSYHKQ IATSDARLAR DLAA VEGDN RERTRRMVDW LAAHPPCPAA DLRTVAAFER VRELVARPSP TLNRINRYLR ASFRRLYRQR NIVLHGGSTR SVALA ATVR TAGPLVGAAL DRLAHGYAVA GTAPLDLASR AELALRVVGD RDGWHLHELL GALESGHHHH HH

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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: 1702 / 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 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: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 245988
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
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-9hxl:
Putative bacterial antiviral defense protein Thr1ApeA from Thermoactinospora rubra strain YIM 77501

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