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- EMDB-75498: KpSwz DUF4062 (Hexamer, catalytic mutant E97A) -

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Basic information

Entry
Database: EMDB / ID: EMD-75498
TitleKpSwz DUF4062 (Hexamer, catalytic mutant E97A)
Map data
Sample
  • Complex: Hexamer of KpSwz DUF4062 domain in the inactive state
    • Protein or peptide: KpSwz DUF4062
  • Ligand: water
KeywordsDUF4062 / TIR / Anti-phage defense / bacterial immunity / NADase / HYDROLASE
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsOsinski A / Lopez VA / Tagliabracci VS
Funding support United States, 6 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Welch FoundationI-1911 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR150033 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
National Institutes of Health/National Cancer Institute (NIH/NCI)K00CA264162 United States
CitationJournal: Biorxiv / Year: 2026
Title: TIR-like NADases act in bacterial immunity and the RNA vault
Authors: Osinski A / Mayro B / Lopez VA / Schrad J / Choi H / Tomchick DR / Pawlowski K / Forsberg K / Shahmoradian SH / Tagliabracci VS
History
DepositionFeb 10, 2026-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75498.png

Downloads & links

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Map

FileDownload / File: emd_75498.map.gz / Format: CCP4 / Size: 144.7 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 336 pix.
= 278.88 Å		0.83 Å/pix.
x 336 pix.
= 278.88 Å		0.83 Å/pix.
x 336 pix.
= 278.88 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy SOFTWARE: 0.125
Minimum - Maximum-1.2215782 - 2.020387
Average (Standard dev.)0.0003981228 (±0.048882965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 278.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75498_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_75498_additional_1.map
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Half map: #1

Fileemd_75498_half_map_1.map
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Half map: #2

Fileemd_75498_half_map_2.map
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Sample components

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Entire : Hexamer of KpSwz DUF4062 domain in the inactive state

EntireName: Hexamer of KpSwz DUF4062 domain in the inactive state
Components
  • Complex: Hexamer of KpSwz DUF4062 domain in the inactive state
    • Protein or peptide: KpSwz DUF4062
  • Ligand: water

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Supramolecule #1: Hexamer of KpSwz DUF4062 domain in the inactive state

SupramoleculeName: Hexamer of KpSwz DUF4062 domain in the inactive state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Klebsiella pneumoniae (bacteria) / Strain: MS5452

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Macromolecule #1: KpSwz DUF4062

MacromoleculeName: KpSwz DUF4062 / type: protein_or_peptide / ID: 1 / Details: E97A catalytic dead mutation / Number of copies: 6 / Enantiomer: LEVO / EC number: NAD+ glycohydrolase
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 #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 203 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTrisTris
150.0 mMNaClSodium chloride
1.0 mMDTTDithiothreitol
GridModel: Quantifoil R1.2/1.3 / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
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: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 53724
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-10wc:
KpSwz DUF4062 (Hexamer, catalytic mutant E97A)

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