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- EMDB-52483: Bacterial antiviral defense protein Ec1ApeA from Escherichia coli... -

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Basic information

Entry
Database: EMDB / ID: EMD-52483
TitleBacterial antiviral defense protein Ec1ApeA from Escherichia coli strain NCTC8008
Map datasharpened map (phenix.auto_sharpen b_iso_to_d_cut, 3.23)
Sample
  • Complex: Bacterial antiviral defense protein Ec1ApeA from Escherichia coli strain NCTC8008
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec1ApeA from Escherichia coli strain NCTC8008
KeywordsApeA / HEPN domain / bacterial antiviral defence / RNA BINDING PROTEIN
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 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_52483.png

Downloads & links

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Map

FileReleased
Annotationsharpened map (phenix.auto_sharpen b_iso_to_d_cut, 3.23)
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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-23.378990000000002 - 34.036679999999997
Average (Standard dev.)0.000000000008246 (±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_52483_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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

Fileemd_52483_additional_1.map
Annotationunsharpened map, input to phenix.auto_sharpen
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: half map 1

Fileemd_52483_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_52483_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Sample components

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Entire : Bacterial antiviral defense protein Ec1ApeA from Escherichia coli...

EntireName: Bacterial antiviral defense protein Ec1ApeA from Escherichia coli strain NCTC8008
Components
  • Complex: Bacterial antiviral defense protein Ec1ApeA from Escherichia coli strain NCTC8008
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec1ApeA from Escherichia coli strain NCTC8008

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Supramolecule #1: Bacterial antiviral defense protein Ec1ApeA from Escherichia coli...

SupramoleculeName: Bacterial antiviral defense protein Ec1ApeA from Escherichia coli strain NCTC8008
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: NCTC8008

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Bacterial antivi...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec1ApeA from Escherichia coli strain NCTC8008
type: protein_or_peptide / ID: 1
Details: ec1ApeA protein fused to an N-terminal MBP (maltose-binding protein)
Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: NCTC8008
Molecular weightTheoretical: 119.518508 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGGSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKGSMGGSH HHHHHHHHHG MASMKIEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKV TVEHPDKLEE KFPQVAATGD GPDIIFWAHD RFGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA Y PIAVEALS ...String:
MGGSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKGSMGGSH HHHHHHHHHG MASMKIEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKV TVEHPDKLEE KFPQVAATGD GPDIIFWAHD RFGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA Y PIAVEALS LIYNKDLLPN PPKTWEEIPA LDKELKAKGK SALMFNLQEP YFTWPLIAAD GGYAFKYENG KYDIKDVGVD NA GAKAGLT FLVDLIKNKH MNADTDYSIA EAAFNKGETA MTINGPWAWS NIDTSKVNYG VTVLPTFKGQ PSKPFVGVLS AGI NAASPN KELAKEFLEN YLLTDEGLEA VNKDKPLGAV ALKSYEEELA KDPRIAATME NAQKGEIMPN IPQMSAFWYA VRTA VINAA SGRQTVDEAL KDAQTNSSSN NNNNNNNNNL GIEENLYFQS NAGGGGMKIV SNTVWDGLKL PDYRARFFIE VWKEI LYVN TPSFYQSKMI NTMSGAEELV EAIDDYIQDD KSKKSLLSMI EDYKGNLKKD SIAKDTFKNL HATLLKKIET VPDPIS SNY ILELKTIVKL VLSKESDYYH ELKKQLKSSI LSNADLNKKA RLMDSIYQLT KSFIGYLLWK GYSPTYLYNR MEYLTRI KN YGSRDFSAQF NSCLDKLTIR IHDYTVYFLI TPLSKYLIEL NNILDVSFIN REGIINEKNY NKISQGVESS VLAKIVVN T TDYVSAAWQA NEKLDKVIDY LEIEKPEYNI RYSPVCLTEF SNGRFTHRQT INIGRLKQFI TSKNYSILEN IPNESKVLL RESIKLDRYD VLTRSLRYLR VAKESTSLEQ KLLGVWIALE CIFESTSGNI ISGITNHIPT FYSTQSLEIR IRYSKDLLEA RLKPISDSL LEITANQKSK FRDLSLKEYF DIVKIEKNRN KIFDELVSKG DEFAVFRLIK IFESFGTSKK INDRFNDTKK D VESQLYRI YKVRNKITHR AYYGNIRPQL VDHLYSYLLS AYSTLIYSLR YNAINKFEPQ DMFNAYIISC ESLIFNVEEE KK LENITMD EIILS

UniProtKB: Maltose/maltodextrin-binding periplasmic protein

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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: 2480 / 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: D5 (2x5 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 214179
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
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-9hxn:
Bacterial antiviral defense protein Ec1ApeA from Escherichia coli strain NCTC8008

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