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- PDB-9hxj: Bacterial antiviral defense protein Ec3ApeA from Escherichia coli... -

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Basic information

Entry
Database: PDB / ID: 9hxj
TitleBacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
ComponentsMaltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
KeywordsRNA BINDING PROTEIN / ApeA / HEPN domain / bacterial antiviral defence
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsSasnauskas, G. / Juozapaitis, J. / Puteikiene, R. / Tamulaitiene, G.
Funding supportLithuania, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
B: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
C: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
D: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
E: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
F: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
G: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
H: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
I: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
J: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
K: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
L: Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,404,24324
Polymers1,403,45812
Non-polymers78512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Maltose/maltodextrin-binding periplasmic protein,Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 116954.859 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: ec3ApeA protein fused to N-terminal MBP (maltose binding protein)
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Escherichia coli (E. coli)
Gene: malE, b4034, JW3994 / Strain: KK-NP016 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: P0AEX9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacterial antiviral defense protein Ec3ApeA from Escherichia coli strain KK-NP016
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli) / Strain: KK-NP016
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21-AI
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 92000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1496

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPU3.5.1image acquisition
4cryoSPARCCTF correction
9PHENIX1.21rc1_4903model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D6 (2x6 fold dihedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60670 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE

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