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

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Basic information

Entry
Database: PDB / ID: 10wc
TitleKpSwz DUF4062 (Hexamer, catalytic mutant E97A)
ComponentsKpSwz DUF4062
KeywordsHYDROLASE / DUF4062 / TIR / Anti-phage defense / bacterial immunity / NADase
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsOsinski, A. / Lopez, V.A. / Tagliabracci, V.S.
Funding support United States, 6items
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, V.A. / Schrad, J. / Choi, H. / Tomchick, D.R. / Pawlowski, K. / Forsberg, K. / Shahmoradian, S.H. / Tagliabracci, V.S.
History
DepositionFeb 10, 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
Revision 1.0May 20, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 20, 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: KpSwz DUF4062
B: KpSwz DUF4062
C: KpSwz DUF4062
D: KpSwz DUF4062
E: KpSwz DUF4062
F: KpSwz DUF4062


Theoretical massNumber of molelcules
Total (without water)225,4416
Polymers225,4416
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
KpSwz DUF4062


Mass: 37573.559 Da / Num. of mol.: 6 / Mutation: E97A
Source method: isolated from a genetically manipulated source
Details: E97A catalytic dead mutation / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: MS5452 / Gene: MS5452_35130 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: NAD+ glycohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
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: Hexamer of KpSwz DUF4062 domain in the inactive state / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Klebsiella pneumoniae (bacteria) / Strain: MS5452
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta(DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTris1
2150 mMSodium chlorideNaCl1
31 mMDithiothreitolDTT1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2crYOLOparticle selection
3SerialEMimage acquisition
8UCSF Chimeramodel fitting
13cryoSPARC3D reconstruction
14PHENIX2.0_5885model refinement
15ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53724 / 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: 83.17 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318430
ELECTRON MICROSCOPYf_angle_d0.430511340
ELECTRON MICROSCOPYf_chiral_restr0.03831290
ELECTRON MICROSCOPYf_plane_restr0.0041422
ELECTRON MICROSCOPYf_dihedral_angle_d3.87091092

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