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Basic information

Entry
Database: PDB / ID: 9hxe
TitleBacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 saturated with pdApdG dinucleotide (HEPN active site mutant R502A)
Components
  • Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
  • DNA (5'-D(P*AP*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: 3.2 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 (HEPN active site mutant R502A)
B: DNA (5'-D(P*AP*G)-3')
C: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
D: DNA (5'-D(P*AP*G)-3')
E: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
F: DNA (5'-D(P*AP*G)-3')
G: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
H: DNA (5'-D(P*AP*G)-3')
I: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
J: DNA (5'-D(P*AP*G)-3')
K: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
L: DNA (5'-D(P*AP*G)-3')
M: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
N: DNA (5'-D(P*AP*G)-3')
O: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
P: DNA (5'-D(P*AP*G)-3')
Q: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
R: DNA (5'-D(P*AP*G)-3')
S: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)
T: DNA (5'-D(P*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)698,50830
Polymers697,85420
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_2DADADGDGBB0 - 11 - 2
d_2ens_2DADADGDGDD0 - 11 - 2
d_3ens_2DADADGDGFF0 - 11 - 2
d_4ens_2DADADGDGHH0 - 11 - 2
d_5ens_2DADADGDGJJ0 - 11 - 2
d_6ens_2DADADGDGLL0 - 11 - 2
d_7ens_2DADADGDGNN0 - 11 - 2
d_8ens_2DADADGDGPP0 - 11 - 2
d_9ens_2DADADGDGRR0 - 11 - 2
d_10ens_2DADADGDGTT0 - 11 - 2

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.808684273809, 0.588242901561, 0.000184545593157), (0.588242920309, -0.808684278413, -6.74801320828E-5), (0.000109544411143, 0.000163127760259, -0.999999980695)-69.8674071905, 214.798977704, 351.958365025
2given(0.30855134308, 0.951207662601, 0.000226477953178), (-0.951207689506, 0.308551336918, 6.25376213559E-5), (-1.03938106011E-5, -0.000234723637629, 0.999999972398)-45.7415413853, 289.088013727, 0.037623205034
3given(0.809266484085, -0.587441659765, -0.000232614660599), (-0.587441703356, -0.809266380972, -0.000412053030593), (5.3809891659E-5, 0.000470108259772, -0.999999888051)136.999282441, 421.878396525, 351.913120494
4given(-0.809259802059, 0.587450906877, -6.91400666239E-5), (-0.587450884949, -0.809259795655, -0.0002022600754), (-0.000174770140907, -0.000123064555259, 0.999999977155)215.045904708, 421.838874595, 0.0564704999256
5given(-0.308534746144, -0.951212970877, -0.000440973967782), (-0.951213060119, 0.308534785347, -2.2122531047E-5), (0.000157099046974, 0.000412634627826, -0.999999902526)397.7681219, 289.112698835, 351.905306682
6given(-0.80864333431, -0.588299198488, -0.000104569131513), (0.588299207551, -0.808643316237, -0.000171755781805), (1.64846594885E-5, -0.000200407105289, 0.999999979783)421.861966064, 214.799037449, 0.0232285253404
7given(-0.999999969346, -0.00024421640819, -4.08147485168E-5), (-0.000244220000812, 0.999999966303, 8.80408318513E-5), (4.07932461257E-5, 8.80507969305E-5, -0.999999995291)352.038269317, 0.0256392137302, 351.983212286
8given(0.309514249514, -0.950894770367, -0.000255020947959), (0.950894787571, 0.309514283554, -0.000106046157324), (0.000179771362416, -0.000209675293338, 0.999999961859)288.910974126, -45.8014136293, -0.00566045494585
9given(-0.309446816452, 0.950916726608, 0.000216437263074), (0.950916751164, 0.309446811281, 5.78295514093E-5), (-1.19847331734E-5, 0.000223708989614, -0.999999974905)63.0761352345, -45.8197872308, 351.968521263
10given(0.80867304783, 0.588258333237, 0.00018732446593), (0.588258352725, -0.808673052317, -7.0041015342E-5), (0.000110282036694, 0.000166835463103, -0.999999980002)-69.8681322479, 214.793899849, 351.957548346
11given(0.308532086767, 0.951213911805, 0.000213129636491), (-0.951213935666, 0.308532077718, 7.49292914587E-5), (5.51645486737E-6, -0.000225849970987, 0.999999974481)-45.7363882363, 289.091119711, 0.0324685489801
12given(0.809271351281, -0.587434950519, -0.000242703898785), (-0.587434999304, -0.80927125231, -0.000402214130373), (3.9861349663E-5, 0.000468073137405, -0.999999889659)136.998415722, 421.876339615, 351.916645994
13given(-0.809268384821, 0.587439083232, -6.94318774739E-5), (-0.587439063114, -0.809268379741, -0.000191517256876), (-0.000168693744788, -0.000114201864084, 0.99999997925)215.04997664, 421.836156887, 0.0535375520946
14given(-0.308541738259, -0.95121070584, -0.000434565830408), (-0.951210789722, 0.308541783238, -3.88980464481E-5), (0.000171081954466, 0.000401362035862, -0.99999990482)397.768329922, 289.113333811, 351.904225441
15given(-0.808651018105, -0.588288637015, -0.000102357701451), (0.58828864586, -0.808651003311, -0.000154905033462), (8.35721302672E-6, -0.000185479986598, 0.999999982764)421.861439292, 214.800359939, 0.0223381864393
16given(-0.999999969676, -0.000242313509947, -4.39552306868E-5), (-0.000242318312117, 0.99999996467, 0.00010927897311), (4.39287493624E-5, 0.000109289620954, -0.999999993063)352.038449286, 0.0220968121784, 351.978628859
17given(0.309501963632, -0.95089876853, -0.000257906308696), (0.950898786228, 0.309501998327, -0.000106680570477), (0.000181264941015, -0.000212224949855, 0.999999961052)288.914858376, -45.799908809, -0.00549877206242
18given(-0.309458790559, 0.950912832631, 0.000204165038035), (0.950912854512, 0.309458785282, 5.77456658619E-5), (-8.2695699705E-6, 0.000212013063027, -0.999999977491)63.0813605225, -45.8210667775, 351.969851904

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Components

#1: Protein
Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (HEPN active site mutant R502A)


Mass: 69187.930 Da / Num. of mol.: 10 / Mutation: R502A
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*AP*G)-3')


Mass: 597.455 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 pdApdG dinucleotide (HEPN active site mutant R502A)
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: 1522

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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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61743 / Algorithm: FOURIER SPACE / 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: 70.31 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004447370
ELECTRON MICROSCOPYf_angle_d0.712464370
ELECTRON MICROSCOPYf_chiral_restr0.05227620
ELECTRON MICROSCOPYf_plane_restr0.00548070
ELECTRON MICROSCOPYf_dihedral_angle_d14.842117380
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints0.000831120889958
ens_1d_3AAELECTRON MICROSCOPYNCS constraints0.000811019515491
ens_1d_4AAELECTRON MICROSCOPYNCS constraints0.000781744761535
ens_1d_5AAELECTRON MICROSCOPYNCS constraints0.000654687561241
ens_1d_6AAELECTRON MICROSCOPYNCS constraints0.000759469321636
ens_1d_7AAELECTRON MICROSCOPYNCS constraints0.000868047771549
ens_1d_8AAELECTRON MICROSCOPYNCS constraints0.000786387164866
ens_1d_9AAELECTRON MICROSCOPYNCS constraints0.000773152166451
ens_1d_10AAELECTRON MICROSCOPYNCS constraints0.000749333627805
ens_2d_2BBELECTRON MICROSCOPYNCS constraints0.000457689189353
ens_2d_3BBELECTRON MICROSCOPYNCS constraints0.000499917628245
ens_2d_4BBELECTRON MICROSCOPYNCS constraints0.00046559778619
ens_2d_5BBELECTRON MICROSCOPYNCS constraints0.000520095226534
ens_2d_6BBELECTRON MICROSCOPYNCS constraints0.000469881174884
ens_2d_7BBELECTRON MICROSCOPYNCS constraints0.000494942835327
ens_2d_8BBELECTRON MICROSCOPYNCS constraints0.000514736399227
ens_2d_9BBELECTRON MICROSCOPYNCS constraints0.000516520806982
ens_2d_10BBELECTRON MICROSCOPYNCS constraints0.000472341059674

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