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- PDB-11cq: KpSwz in complex with bacteriophage Bas14 Portal -

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Basic information

Entry
Database: PDB / ID: 11cq
TitleKpSwz in complex with bacteriophage Bas14 Portal
Components
  • KpSwz
  • Portal protein
KeywordsHYDROLASE / Bacteriophage / phage / portal protein / bacterial immunity / TIR / DUF4062 / NADase
Function / homologyDomain of unknown function DUF4055 / Domain of unknown function (DUF4055) / Portal protein
Function and homology information
Biological speciesEscherichia phage TheodorHerzl (virus)
Klebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsOsinski, A. / Tagliabracci, V.S.
Funding support United States, 5items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Welch FoundationI-1911 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137419 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM158265 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR150033 United States
CitationJournal: bioRxiv / Year: 2026
Title: TIR-like NADases act in bacterial immunity and the RNA vault.
Authors: Adam Osinski / Benjamin Mayro / Victor A Lopez / Jason Schrad / Hannah Choi / Diana R Tomchick / Krzysztof Pawłowski / Kevin Forsberg / Sarah H Shahmoradian / Vincent S Tagliabracci /
Abstract: Across all domains of life, organisms exploit NAD metabolism as a central line of defense against invading pathogens. Here, we show that domain of unknown function 4062 (DUF4062) is a widespread ...Across all domains of life, organisms exploit NAD metabolism as a central line of defense against invading pathogens. Here, we show that domain of unknown function 4062 (DUF4062) is a widespread family of TIR-like NADases that hydrolyze NAD to ADP-ribose and nicotinamide. In bacteria, DUF4062 homologs form a previously unrecognized antiphage defense system, which we name Swarożyc, that assembles with the phage portal into a supramolecular NADase complex to induce abortive infection. In eukaryotes, DUF4062 is found in TEP1, which we demonstrate functions as an active NADase within the RNA vault, an enigmatic organelle-like structure. Single-particle cryo-electron microscopy reveals ADP-ribose bound within the shoulder of both reconstituted and human brain vaults, while cryo-electron tomography positions TEP1 along the central axis at the shoulder. Thus, TEP1, like bacterial Swarożyc, functions by depleting NAD, providing new insight into the long-standing mystery of vault function.
History
DepositionFeb 17, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jun 3, 2026Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.1Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein
a: KpSwz
b: KpSwz
c: KpSwz
d: KpSwz
e: KpSwz
f: KpSwz
g: KpSwz
h: KpSwz
i: KpSwz
j: KpSwz
k: KpSwz
l: KpSwz
m: KpSwz
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,164,93937
Polymers1,164,64725
Non-polymers29212
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "D" and resid 260 through 270)
d_2ens_1(chain "B" and resid 260 through 270)
d_3ens_1(chain "C" and resid 260 through 270)
d_4ens_1(chain "A" and resid 260 through 270)
d_5ens_1(chain "E" and resid 260 through 270)
d_6ens_1(chain "F" and resid 260 through 270)
d_7ens_1(chain "G" and resid 260 through 270)
d_8ens_1(chain "H" and resid 260 through 270)
d_9ens_1(chain "I" and resid 260 through 270)
d_10ens_1(chain "J" and resid 260 through 270)
d_11ens_1(chain "K" and resid 260 through 270)
d_12ens_1(chain "L" and resid 260 through 270)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 260 - 270 / Label seq-ID: 260 - 270

Dom-IDAuth asym-IDLabel asym-ID
d_1DD
d_2BB
d_3CC
d_4AA
d_5EE
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ
d_11KK
d_12LL

NCS oper:
IDCodeMatrixVector
1given(0.497790319957, 0.867296167896, 0.00146782491302), (-0.867211798847, 0.497764249016, -0.0132078894071), (-0.0121857826343, 0.0053018444107, 0.999911694675)-66.6623348431, 251.67905601, 0.82472458499
2given(0.851210076445, 0.507809571603, 0.132555063074), (-0.509480164267, 0.860159853714, -0.0235581891712), (-0.125981617614, -0.0474812073041, 0.990895638792)-86.4868976308, 121.941414405, 38.618375945
3given(-0.00411253818035, 0.997901686003, 0.0646166549883), (-0.995604657566, 0.00196003484258, -0.0936350580499), (-0.0935652331922, -0.0647177204139, 0.99350750566)-9.67365221706, 378.251494886, 33.0216470121
4given(0.862033794721, -0.506562644659, 0.0170887037006), (0.502866796056, 0.85899069311, 0.0962287616759), (-0.0634249334429, -0.0743591029101, 0.995212540934)114.673696339, -82.6855793073, 28.4277618377
5given(0.496500924403, -0.867918241355, -0.0143093811993), (0.867565651576, 0.495621642243, 0.0410977851607), (-0.0285774784108, -0.032819415947, 0.999052658104)251.530579366, -73.5503647139, 11.8194885903
6given(-0.0166523891572, -0.998101900379, -0.0592899181521), (0.992360542645, -0.0237481462074, 0.12106435872), (-0.122242592152, -0.0568209645363, 0.990872406848)377.541769462, -14.8695238822, 38.3555855347
7given(-0.492619375858, -0.869981710985, 0.0214003056263), (0.869920849164, -0.491616031395, 0.0393877374903), (-0.023745877931, 0.0380197347018, 0.998994811325)425.457715404, 105.772561499, -1.85106215719
8given(-0.862074028909, -0.500016523164, -0.0825339035972), (0.501465717339, -0.865169946626, 0.00361908669154), (-0.0732154561146, -0.038268002527, 0.996581686049)442.938567925, 247.322385809, 24.2633163853
9given(-0.999886467261, -0.00371479220467, 0.0146031814086), (0.00362851855516, -0.999975834603, -0.00592992946596), (0.0146248569726, -0.00587626831012, 0.9998757838)362.065128107, 363.431033416, -2.35314012989
10given(-0.86092061573, 0.50775463433, -0.0316373944451), (-0.503439441568, -0.859255910456, -0.0907083734868), (-0.0732422151788, -0.062165196562, 0.99537483706)250.936068179, 445.163639912, 28.502720428
11given(-0.495675139449, 0.868439241234, 0.0109288799954), (-0.868418474049, -0.495404121755, -0.0205939330375), (-0.0124703673852, -0.0196987419189, 0.999728187811)112.302625929, 433.570913568, 5.75578548161

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Components

#1: Protein
Portal protein


Mass: 56349.219 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage TheodorHerzl (virus) / Gene: bas14_0003 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAE7VZF8
#2: Protein
KpSwz


Mass: 37573.559 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: MS5452 / Gene: MS5452_35130 / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
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

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1KpSwz in complex with bacteriophage Bas14 PortalCOMPLEXonly auxilliary domain of KpSwz is visible on the surface of the Portal#1-#20RECOMBINANT
2Bas14 bacteriophage portal proteinCOMPLEX#11RECOMBINANT
3KpSwz anti-phage defense systemCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Escherichia phage TheodorHerzl (virus)2851978
43Klebsiella pneumoniae (bacteria)573
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Escherichia coli BL21(DE3) (bacteria)469008
43Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTris1
2150 mMSodium ChlorideNaCl1
31 mMDithiothreitolDTT1
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
14ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204790 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 96.05 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001447496
ELECTRON MICROSCOPYf_angle_d0.379664513
ELECTRON MICROSCOPYf_chiral_restr0.03727342
ELECTRON MICROSCOPYf_plane_restr0.00338349
ELECTRON MICROSCOPYf_dihedral_angle_d10.216717422
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DDELECTRON MICROSCOPYNCS constraints1.86222829554E-13
ens_1d_3DDELECTRON MICROSCOPYNCS constraints3.43075777309E-13
ens_1d_4DDELECTRON MICROSCOPYNCS constraints2.52287026291E-11
ens_1d_5DDELECTRON MICROSCOPYNCS constraints2.29685874448E-13
ens_1d_6DDELECTRON MICROSCOPYNCS constraints1.52558751127E-13
ens_1d_7DDELECTRON MICROSCOPYNCS constraints5.74432907055E-12
ens_1d_8DDELECTRON MICROSCOPYNCS constraints2.13473025616E-12
ens_1d_9DDELECTRON MICROSCOPYNCS constraints2.94399577075E-11
ens_1d_10DDELECTRON MICROSCOPYNCS constraints2.34005090414E-13
ens_1d_11DDELECTRON MICROSCOPYNCS constraints1.97834550481E-13
ens_1d_12DDELECTRON MICROSCOPYNCS constraints1.99394132862E-13

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