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Basic information

Entry
Database: PDB / ID: 9hxi
TitleBacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 saturated with pdCpdG dinucleotide
Components
  • Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1
  • DNA (5'-D(P*CP*G)-3')
KeywordsRNA BINDING PROTEIN / ApeA / HEPN domain / bacterial antiviral defence
Function / homologyDNA
Function and homology information
Biological speciesEscherichia coli 2-156-04_S4_C1 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 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 7, 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

Downloads & links

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Assembly

Deposited unit
A: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1
B: DNA (5'-D(P*CP*G)-3')
C: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1
D: DNA (5'-D(P*CP*G)-3')
E: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1
F: DNA (5'-D(P*CP*G)-3')
G: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1
H: DNA (5'-D(P*CP*G)-3')
I: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1
J: DNA (5'-D(P*CP*G)-3')
K: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1
L: DNA (5'-D(P*CP*G)-3')
M: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1
N: DNA (5'-D(P*CP*G)-3')
O: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1
P: DNA (5'-D(P*CP*G)-3')
Q: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1
R: DNA (5'-D(P*CP*G)-3')
S: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1
T: DNA (5'-D(P*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)699,12930
Polymers698,47520
Non-polymers65410
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "C"
d_3ens_1chain "E"
d_4ens_1chain "G"
d_5ens_1chain "I"
d_6ens_1chain "K"
d_7ens_1chain "M"
d_8ens_1chain "O"
d_9ens_1chain "Q"
d_10ens_1chain "S"
d_1ens_2chain "B"
d_2ens_2chain "D"
d_3ens_2chain "F"
d_4ens_2chain "H"
d_5ens_2chain "J"
d_6ens_2chain "L"
d_7ens_2chain "N"
d_8ens_2chain "P"
d_9ens_2chain "R"
d_10ens_2chain "T"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1METMETGLNGLNAA1 - 5831 - 583
d_2ens_1METMETGLNGLNCC1 - 5831 - 583
d_3ens_1METMETGLNGLNEE1 - 5831 - 583
d_4ens_1METMETGLNGLNGG1 - 5831 - 583
d_5ens_1METMETGLNGLNII1 - 5831 - 583
d_6ens_1METMETGLNGLNKK1 - 5831 - 583
d_7ens_1METMETGLNGLNMM1 - 5831 - 583
d_8ens_1METMETGLNGLNOO1 - 5831 - 583
d_9ens_1METMETGLNGLNQQ1 - 5831 - 583
d_10ens_1METMETGLNGLNSS1 - 5831 - 583
d_1ens_2DCDCDGDGBB0 - 11 - 2
d_2ens_2DCDCDGDGDD0 - 11 - 2
d_3ens_2DCDCDGDGFF0 - 11 - 2
d_4ens_2DCDCDGDGHH0 - 11 - 2
d_5ens_2DCDCDGDGJJ0 - 11 - 2
d_6ens_2DCDCDGDGLL0 - 11 - 2
d_7ens_2DCDCDGDGNN0 - 11 - 2
d_8ens_2DCDCDGDGPP0 - 11 - 2
d_9ens_2DCDCDGDGRR0 - 11 - 2
d_10ens_2DCDCDGDGTT0 - 11 - 2

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.309604013656, -0.950865328531, 0.000694064050817), (-0.950861701673, 0.309604753049, 0.00263081382545), (-0.0027164351815, 0.000154551595113, -0.99999629854)397.760464675, 288.488568303, 352.502289197
2given(0.309533463293, 0.95088827076, -0.000729131560419), (-0.950884828332, 0.30953430614, 0.00256058008398), (0.00266051679983, -9.92650827715E-5, 0.999996455892)-45.7480535, 288.512574287, -0.502620825763
3given(-0.999996377716, 0.000827708142351, 0.00256114326544), (0.000827815122849, 0.999999656532, 4.07108062247E-5), (-0.00256110868911, 4.28308118855E-5, -0.999996719439)351.498730852, -0.168906681922, 352.49147553
4given(-0.808654093569, 0.58827861072, 0.00261402458732), (-0.58827757469, -0.808658136331, 0.00123031003628), (0.00283761733, -0.000542876797216, 0.999995826598)214.408583368, 421.701083334, -0.470722297251
5given(-0.308191606529, 0.951323448744, 0.00127653210995), (0.951320283885, 0.308193927877, -0.00249405083252), (-0.00276606848437, 0.000445745356388, -0.99999607508)62.6114408187, -45.341122014, 352.469415344
6given(-0.809507331626, -0.587106536677, 0.00194798235458), (0.587104645227, -0.809509672899, -0.00149165548651), (0.00245267124527, -6.38365633916E-5, 0.99999699016)421.548964493, 215.369255243, -0.469914625361
7given(0.809483651646, 0.587139106659, -0.00197158565068), (0.587135929136, -0.809485928978, -0.00198280193406), (-0.00276015139824, 0.000447456977191, -0.999996090666)-69.5470883622, 215.424557914, 352.469298257
8given(0.308175968691, -0.951328889574, -0.000957174203985), (0.951326090122, 0.308177392332, -0.00231627060927), (0.00249851459687, -0.000196765854279, 0.999996859349)289.351114508, -45.3628711841, -0.456494293359
9given(0.808496967804, -0.588494884867, -0.00253446984494), (-0.588493505476, -0.808500836625, 0.00133835288441), (-0.00283673481666, 0.000409464794673, -0.999995892629)137.641153749, 421.700261452, 352.487188505
10given(-0.309594212533, -0.950868527694, 0.000683086085425), (-0.950864879103, 0.309594920724, 0.00263946016917), (-0.00272125958743, 0.000167639024552, -0.999996283315)397.760540373, 288.489224724, 352.501523805
11given(0.309532518048, 0.950888580846, -0.000726007486304), (-0.950885157293, 0.309533353295, 0.00255359308739), (0.00265290603868, -0.000100070355597, 0.999996476032)-45.7483701168, 288.513825643, -0.50100139001
12given(-0.999996396973, 0.000820718884854, 0.00255586812278), (0.000820781663472, 0.999999662882, 2.35137321053E-5), (-0.00255584796299, 2.56114570741E-5, -0.999996733487)351.500385532, -0.164983917416, 352.492795277
13given(-0.808655134587, 0.588277179965, 0.00261396964098), (-0.588276093416, -0.808659186705, 0.00124806806161), (0.00284802052363, -0.00052847920237, 0.999995804736)214.408924996, 421.698325154, -0.474648083515
14given(-0.308212496025, 0.951316696728, 0.00126484055812), (0.951313530139, 0.308214784439, -0.00249279520903), (-0.00276128026384, 0.000434949302952, -0.999996093068)62.6181845629, -45.342732904, 352.469839791
15given(-0.809500698291, -0.587115676815, 0.00194974469119), (0.58711376972, -0.809503043494, -0.00149799166045), (0.00245781864914, -6.79033395382E-5, 0.999996977254)421.548656828, 215.367411597, -0.470329355697
16given(0.809488576552, 0.587132324551, -0.0019692379514), (0.58712914042, -0.809490846134, -0.00198557151797), (-0.00275987331642, 0.000451100476037, -0.999996089796)-69.5474911788, 215.426972674, 352.468773386
17given(0.308195952395, -0.951322417328, -0.000955623479699), (0.951319612727, 0.308197372479, -0.0023181970481), (0.00249987346516, -0.00019464441154, 0.999996856368)289.346105078, -45.3639849431, -0.457026284493
18given(0.808508570546, -0.588478885473, -0.00254807880261), (-0.588477517807, -0.808512477113, 0.00133618402934), (-0.00284646959294, 0.000419170849389, -0.999995860945)137.638784067, 421.699007457, 352.487763289

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Components

#1: Protein
Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1


Mass: 69274.047 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 2-156-04_S4_C1 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: DNA chain
DNA (5'-D(P*CP*G)-3')


Mass: 573.430 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / 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 Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 saturated with pdCpdG dinucleotide
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli 2-156-04_S4_C1 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
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: 1084

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77371 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 89.23 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003746800
ELECTRON MICROSCOPYf_angle_d0.569563630
ELECTRON MICROSCOPYf_chiral_restr0.04147600
ELECTRON MICROSCOPYf_plane_restr0.00527940
ELECTRON MICROSCOPYf_dihedral_angle_d12.037516950
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints0.00128820715391
ens_1d_3AAELECTRON MICROSCOPYNCS constraints0.00108037440061
ens_1d_4AAELECTRON MICROSCOPYNCS constraints0.00109051792703
ens_1d_5AAELECTRON MICROSCOPYNCS constraints0.0012786349881
ens_1d_6AAELECTRON MICROSCOPYNCS constraints0.00126810202786
ens_1d_7AAELECTRON MICROSCOPYNCS constraints0.00104672608219
ens_1d_8AAELECTRON MICROSCOPYNCS constraints0.00115301084089
ens_1d_9AAELECTRON MICROSCOPYNCS constraints0.00110258657186
ens_1d_10AAELECTRON MICROSCOPYNCS constraints0.00121618790336
ens_2d_2BBELECTRON MICROSCOPYNCS constraints0.000473466445892
ens_2d_3BBELECTRON MICROSCOPYNCS constraints0.000473380327566
ens_2d_4BBELECTRON MICROSCOPYNCS constraints0.000484720301366
ens_2d_5BBELECTRON MICROSCOPYNCS constraints0.000507338090096
ens_2d_6BBELECTRON MICROSCOPYNCS constraints0.000501997222275
ens_2d_7BBELECTRON MICROSCOPYNCS constraints0.000488291999004
ens_2d_8BBELECTRON MICROSCOPYNCS constraints0.000484719033393
ens_2d_9BBELECTRON MICROSCOPYNCS constraints0.000525666794055
ens_2d_10BBELECTRON MICROSCOPYNCS constraints0.000484513432491

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