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- EMDB-75622: KpSwz in complex with bacteriophage Bas14 Portal -

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Basic information

Entry
Database: EMDB / ID: EMD-75622
TitleKpSwz in complex with bacteriophage Bas14 Portal
Map data
Sample
  • Complex: KpSwz in complex with bacteriophage Bas14 Portal
    • Complex: Bas14 bacteriophage portal protein
      • Protein or peptide: Portal protein
    • Complex: KpSwz anti-phage defense system
      • Protein or peptide: KpSwz
  • Ligand: MAGNESIUM ION
KeywordsBacteriophage / phage / portal protein / bacterial immunity / TIR / DUF4062 / NADase / HYDROLASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsOsinski A / Tagliabracci VS
Funding support United States, 5 items
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, 2026-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75622.png

Downloads & links

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Map

FileDownload / File: emd_75622.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 363.44 Å		0.83 Å/pix.
x 440 pix.
= 363.44 Å		0.83 Å/pix.
x 440 pix.
= 363.44 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.587 - 0.99118423
Average (Standard dev.)0.0013424358 (±0.022967141)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 363.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75622_msk_1.map
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Additional map: #1

Fileemd_75622_additional_1.map
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Half map: #1

Fileemd_75622_half_map_1.map
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Half map: #2

Fileemd_75622_half_map_2.map
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Sample components

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Entire : KpSwz in complex with bacteriophage Bas14 Portal

EntireName: KpSwz in complex with bacteriophage Bas14 Portal
Components
  • Complex: KpSwz in complex with bacteriophage Bas14 Portal
    • Complex: Bas14 bacteriophage portal protein
      • Protein or peptide: Portal protein
    • Complex: KpSwz anti-phage defense system
      • Protein or peptide: KpSwz
  • Ligand: MAGNESIUM ION

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Supramolecule #1: KpSwz in complex with bacteriophage Bas14 Portal

SupramoleculeName: KpSwz in complex with bacteriophage Bas14 Portal / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: only auxilliary domain of KpSwz is visible on the surface of the Portal

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Supramolecule #2: Bas14 bacteriophage portal protein

SupramoleculeName: Bas14 bacteriophage portal protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia phage TheodorHerzl (virus)

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Supramolecule #3: KpSwz anti-phage defense system

SupramoleculeName: KpSwz anti-phage defense system / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Klebsiella pneumoniae (bacteria)

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage TheodorHerzl (virus)
Molecular weightTheoretical: 56.349219 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTVNVDNQHP LYARIAPEWK MIRDCVAGER AVKACGPLYL PHPASGDNTD PKARARYKAY KQRAVFMNAT ARTLNALLGV AFAKPVSLD LSGAMADLID DVDGSGMPLP QLLRGAMSEV LQSGRAGFMV DYDRQAHFDE LGNVVPQTAA EMASHRPLIR L YTAEQIIN ...String:
MTVNVDNQHP LYARIAPEWK MIRDCVAGER AVKACGPLYL PHPASGDNTD PKARARYKAY KQRAVFMNAT ARTLNALLGV AFAKPVSLD LSGAMADLID DVDGSGMPLP QLLRGAMSEV LQSGRAGFMV DYDRQAHFDE LGNVVPQTAA EMASHRPLIR L YTAEQIIN WRQTHGVDTL IVLKETDEIS TEDPDDFANH EVTIWTELRM INGAAHARRW YYNADTSEVQ MDLPRGFTRT DL VPLVDAA GNALTQLPFC WCGAVDNNAT PDAAPLADIA SINIKHYNAE ADVAEIAHIV GQPTLVATGL TQSWADKNLK GGI ALGATK GVILGQNMDA KLIQAEERNL SVTLCERREL QMAKLGAALV EKGTAPKTAT EAAYDAQTDN SILSLIAGNV EKAF NRALQ IVQLFTGDTA DQRVTLNKFY TEITVDAQLM TAMMSGVQTG TVRLADFIKW MMAQGVIDDS QTVEQVEDEL RNQNP LPQM SPDAVESTEE DPDKVADDGE NNLEHHHHHH

UniProtKB: Portal protein

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Macromolecule #2: KpSwz

MacromoleculeName: KpSwz / type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria) / Strain: MS5452
Molecular weightTheoretical: 37.573559 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SVDKRYQVFV SSTFTDLQEE RSNVIQSLME MDCIPAGMEL FPSIDEEQWE FIKKIIDDSD YYLLIIGGRY GTVADDGLSF TEKAFDYAV SKGLKVVVLV HENPGALPFD KSEADPLLRE KLQKFIEKAS TGRLRKTWSS AKDLPGLVAL SLNKTIKAYP A IGWVRADK ...String:
SVDKRYQVFV SSTFTDLQEE RSNVIQSLME MDCIPAGMEL FPSIDEEQWE FIKKIIDDSD YYLLIIGGRY GTVADDGLSF TEKAFDYAV SKGLKVVVLV HENPGALPFD KSEADPLLRE KLQKFIEKAS TGRLRKTWSS AKDLPGLVAL SLNKTIKAYP A IGWVRADK VSSEATLFEL NELRKRNEEL SEKVRQLENR PDYAQPENLA SLNDIYELPY EISTVGWYDE DREEHKSLNI KW AELFSLL SPYLTTEAID NEIYDILKNH IEKVAPHSYN HTTIDFQELK TIYLQFKALG LLEHNNVNWK LSPKGMELMM QLR TVKSKS

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTrisTris
150.0 mMNaClSodium Chloride
1.0 mMDTTDithiothreitol
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 204790
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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