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- EMDB-52479: Bacterial antiviral defense protein Ec3ApeA from Escherichia coli... -

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Basic information

Entry
Database: EMDB / ID: EMD-52479
TitleBacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
Map datasharpened map (phenix.auto_sharpen b_iso_to_d_cut, 3.0)
Sample
  • Complex: Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
  • Ligand: ZINC ION
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: 3.0 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 8, 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_52479.png

Downloads & links

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Map

FileReleased
Annotationsharpened map (phenix.auto_sharpen b_iso_to_d_cut, 3.0)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 336 pix.
= 369.6 Å		1.1 Å/pix.
x 336 pix.
= 369.6 Å		1.1 Å/pix.
x 336 pix.
= 369.6 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-22.719414 - 34.545610000000003
Average (Standard dev.)0.000000000003136 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 369.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52479_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_52479_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 1

Fileemd_52479_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_52479_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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Sample components

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Entire : Bacterial antiviral defense protein Ec3ApeA from Escherichia coli...

EntireName: Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
Components
  • Complex: Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
  • Ligand: ZINC ION

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Supramolecule #1: Bacterial antiviral defense protein Ec3ApeA from Escherichia coli...

SupramoleculeName: Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli) / Strain: KK-NP016

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

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
type: protein_or_peptide / ID: 1
Details: ec3ApeA protein fused to N-terminal MBP (maltose binding protein)
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: KK-NP016
Molecular weightTheoretical: 116.954859 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 MKFRSLYKWD CPDTCKALVY FAQLLDEMLF DYTLD TYKP SVMNTPTIGV ETLNTIKDVE DGIIQPKNIE HLTAELIHNL SCDKVAQDLL GDAYQAFLNK LKNTNISPKE RSSIIE MLV IQLPPKLYKE KSEELIIQEL SSPNWERSII RKLTRNYISL LLYIGFSQHN LKNLTQQFFY YGNNKISNNT DASSFFD LI KLEKKKYKIY FIVEPVFLGA EPTFERLSLS VEKEPPEEFS QHVFFRNLQR KKIVCVSNIE AFDSYSAREN AENLLKLA S SFLNIYHHKD KPTWSNEAFV ITDTDSLKVA ERLNPMKKCK DLKHEKAKKR LESLMSEFSL ENSSFAKFLR SIQLHSMAL KSENVENQLL NLWIALESLV PTDTKSKDQA TIEHITASII PFLNITYIDS LIDNLTRDLL LWNRHILNSH LKGIPGAKAK HKLANIMIL PEYESVRESL SAKFRDYTLL SDRFEYIKNI VSSPESIKST LDNHKLRLEW QLRRIYRTRN NIVHSGKGGK F TPLLVEHT HNYLDKVFEI LVMLASKPRK IRSVTQGFRY VKIIYEQRYE TITEKNFTFD MSNINNNLFW D

UniProtKB: Maltose/maltodextrin-binding periplasmic protein

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 12 / 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: 1496 / 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: D6 (2x6 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 60670
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-9hxj:
Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016

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