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Basic information

Entry
Database: PDB / ID: 9hxg
TitleBacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 saturated with pdCpdG 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*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: 2.43 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

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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*CP*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*CP*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*CP*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*CP*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*CP*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*CP*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*CP*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*CP*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*CP*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*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)698,26830
Polymers697,61420
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(0.808527970514, -0.588457612862, 0.000398448625311), (-0.588457641338, -0.808528046168, -5.39468687512E-5), (0.000353902334128, -0.000190852585938, -0.999999919164)137.206776586, 421.915023316, 349.759517346
2given(0.309719453102, 0.950827984154, -7.01404476804E-5), (-0.950827822662, 0.309719355476, -0.000610323754876), (-0.000558589051282, 0.000255720628724, 0.999999811293)-45.8677311166, 288.94107269, 0.0753289091763
3given(-0.309746651957, -0.95081911696, -0.000135734215507), (-0.950818938804, 0.309746677341, -0.000584369843291), (0.000597673240631, -5.19479397167E-5, -0.999999820044)397.904707709, 288.929548624, 349.687083491
4given(-0.808535813821, 0.588446884611, -0.000319000161941), (-0.588446818781, -0.80853587578, -0.000281146042263), (-0.000423362587999, -3.96020135985E-5, 0.999999909598)214.79080419, 421.942325802, 0.0874244567916
5given(-0.999999709629, 0.000610162166728, -0.00045655578852), (0.000610287889545, 0.999999775884, -0.00027528367282), (0.000456387718517, -0.000275562223355, -0.999999857888)351.977282958, -0.070114360358, 349.762076744
6given(-0.809400003641, -0.587257682115, -0.00022114093028), (0.587257609904, -0.809400023819, 0.000317887098948), (-0.000365673115139, 0.000127431124878, 0.999999925022)421.885137485, 215.066171484, 0.0559765173211
7given(-0.308398026557, 0.951257358741, -0.000307664247186), (0.95125730734, 0.308398126787, 0.000361421942375), (0.000438688359806, -0.000181206049561, -0.999999887358)62.9028510222, -45.7802474553, 349.739582463
8given(0.308856231442, -0.951108711219, 0.000218498923616), (0.951108706047, 0.308856271422, 0.000181339772319), (-0.000239958600001, 0.000151808309824, 0.999999959687)289.004771179, -45.7926216764, 0.0235305547996
9given(0.809215397092, 0.587512054384, 0.000164505878584), (0.58751199345, -0.80921539942, 0.000308049466701), (0.000314103465279, -0.00015262919486, -0.999999939022)-69.8694173607, 214.979008904, 349.761805782
10given(0.808511130886, -0.588480743942, 0.000406501120785), (-0.588480774461, -0.808511209151, -5.26007935967E-5), (0.000359615266835, -0.000196689767262, -0.999999915995)137.212817061, 421.917298868, 349.759162816
11given(0.309717030826, 0.950828773011, -7.23213826597E-5), (-0.950828613366, 0.309716932578, -0.000608012568736), (-0.000555716687909, 0.000257077087485, 0.999999812545)-45.8668731958, 288.941225528, 0.0745192787073
12given(-0.309766239626, -0.950812732684, -0.000155416205519), (-0.95081255857, 0.30976627709, -0.000576231613082), (0.000596031054076, -3.07254199251E-5, -0.999999821901)397.910950368, 288.92397029, 349.684191125
13given(-0.808538703613, 0.588442913373, -0.000320095019072), (-0.588442851698, -0.808538766384, -0.000271182561248), (-0.000418384688243, -3.09039706772E-5, 0.999999912)214.79223747, 421.940425568, 0.0850158088277
14given(-0.999999706566, 0.000615151037091, -0.000456571581064), (0.000615276214234, 0.999999773158, -0.000274077814753), (0.000456402878243, -0.000274358651964, -0.999999858212)351.976520429, -0.0713736380797, 349.761843028
15given(-0.809406173645, -0.587249183061, -0.000207507321104), (0.587249120496, -0.809406191764, 0.000295315028583), (-0.000341381219819, 0.00011717131549, 0.999999934865)421.883230916, 215.072298215, 0.0522473620848
16given(-0.308383790533, 0.951261977396, -0.000296812205058), (0.951261922847, 0.308383886506, 0.000364259697027), (0.000438038501038, -0.0001700143628, -0.999999889609)62.8974926683, -45.779499283, 349.738024829
17given(0.308860113324, -0.951107450187, 0.000220446339668), (0.951107441285, 0.308860156224, 0.000197560026789), (-0.000255987904246, 0.0001486497418, 0.999999956187)289.003485003, -45.7953308489, 0.0274250097158
18given(0.809208556299, 0.58752148198, 0.000143608387556), (0.587521423799, -0.809208551925, 0.000309949645561), (0.000298311210438, -0.000166440900883, -0.999999941654)-69.8663379879, 214.975671108, 349.767287705

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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*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 (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: 2040

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 358680 / 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: 89.26 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008247460
ELECTRON MICROSCOPYf_angle_d0.694164470
ELECTRON MICROSCOPYf_chiral_restr0.04337620
ELECTRON MICROSCOPYf_plane_restr0.00598100
ELECTRON MICROSCOPYf_dihedral_angle_d14.182117430
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints0.00049992077718
ens_1d_3AAELECTRON MICROSCOPYNCS constraints0.000501593609024
ens_1d_4AAELECTRON MICROSCOPYNCS constraints0.000498671590669
ens_1d_5AAELECTRON MICROSCOPYNCS constraints0.000498770386055
ens_1d_6AAELECTRON MICROSCOPYNCS constraints0.000496402156922
ens_1d_7AAELECTRON MICROSCOPYNCS constraints0.000499139391429
ens_1d_8AAELECTRON MICROSCOPYNCS constraints0.000501263591532
ens_1d_9AAELECTRON MICROSCOPYNCS constraints0.000499869741447
ens_1d_10AAELECTRON MICROSCOPYNCS constraints0.000501261578087
ens_2d_2BBELECTRON MICROSCOPYNCS constraints0.000505338180681
ens_2d_3BBELECTRON MICROSCOPYNCS constraints0.000489183409166
ens_2d_4BBELECTRON MICROSCOPYNCS constraints0.000496269506426
ens_2d_5BBELECTRON MICROSCOPYNCS constraints0.000471767963943
ens_2d_6BBELECTRON MICROSCOPYNCS constraints0.000505515916161
ens_2d_7BBELECTRON MICROSCOPYNCS constraints0.000457423576224
ens_2d_8BBELECTRON MICROSCOPYNCS constraints0.000490291891397
ens_2d_9BBELECTRON MICROSCOPYNCS constraints0.000499251343302
ens_2d_10BBELECTRON MICROSCOPYNCS constraints0.000460025958909

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