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- EMDB-62051: Cryo-EM structure of depolymerase S2-4 from Klebsiella phage K64-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-62051
TitleCryo-EM structure of depolymerase S2-4 from Klebsiella phage K64-1
Map data
Sample
  • Complex: Depolymerase S2-4 homotrimer
    • Protein or peptide: Depolymerase, capsule K1-specific
KeywordsDepolymerase / Degradation of host capsule / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / adhesion receptor-mediated virion attachment to host cell / lyase activity
Similarity search - Function
: / : / K1 capsule-specific polysaccharide lyase, C-terminal domain / K1 capsule-specific polysaccharide lyase, Rider domain / Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Depolymerase, capsule K1-specific
Similarity search - Component
Biological speciesKlebsiella phage K64-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsZhao R / Du T / Ren Z / Gu J / Ru H
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32072824 China
National Natural Science Foundation of China (NSFC)32222083 China
CitationJournal: Microbiol Res / Year: 2026
Title: Characterization of the phage ΦK64 depolymerase S2-4 and its therapeutic effect against K1 serotype Klebsiella pneumoniae.
Authors: Rihong Zhao / Tianjiao Du / Yalu Ji / Zhuolu Ren / Shanshan Jiang / Heng Ru / Jingmin Gu /
Abstract: The infection rate and drug resistance of Klebsiella pneumoniae containing capsular polysaccharides (CPSs) have been increasing annually, resulting in severe human and animal infections. ...The infection rate and drug resistance of Klebsiella pneumoniae containing capsular polysaccharides (CPSs) have been increasing annually, resulting in severe human and animal infections. Depolymerases derived from bacteriophages can degrade CPSs and thus hold potential for treating bacterial infections. However, little is known about the mechanism by which K. pneumoniae phage depolymerases hydrolyze CPSs. In this study, the S2-4 encoded by the phage ΦK64 was identified as a potent depolymerase against K1 serotype Klebsiella CPSs. Cryo-electron microscopy structural analysis revealed that S2-4 forms a homotrimer with a spindle-like structure comprising a particle-binding domain, a core receptor-binding domain, an insertion domain, and a C-terminal domain. The results of structural assays suggest that S2-4 possesses multiple catalytic centers, which may contribute to its potent depolymerase activity. S2-4 inhibited K. pneumoniae biofilm formation, disrupted preformed biofilms, and enhanced macrophage adhesion and phagocytosis in depolymerase-treated bacteria. In a murine model, a single dose of 5 µg of S2-4 provided full protection against bacterial infection, underscoring the potent depolymerase activity of S2-4. These results indicate that S2-4 is a potent depolymerase against K1 serotype Klebsiella CPSs and has the potential to be a promising candidate for the clinical control of K. pneumoniae infections.
History
DepositionOct 21, 2024-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62051.png

Downloads & links

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Map

FileDownload / File: emd_62051.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-1.9345658 - 2.9839032
Average (Standard dev.)-0.0001956197 (±0.06397549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62051_msk_1.map
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Half map: #2

Fileemd_62051_half_map_1.map
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Half map: #1

Fileemd_62051_half_map_2.map
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Sample components

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Entire : Depolymerase S2-4 homotrimer

EntireName: Depolymerase S2-4 homotrimer
Components
  • Complex: Depolymerase S2-4 homotrimer
    • Protein or peptide: Depolymerase, capsule K1-specific

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Supramolecule #1: Depolymerase S2-4 homotrimer

SupramoleculeName: Depolymerase S2-4 homotrimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella phage K64-1 (virus)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Depolymerase, capsule K1-specific

MacromoleculeName: Depolymerase, capsule K1-specific / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage K64-1 (virus)
Molecular weightTheoretical: 100.996148 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSMETEGL TLDWNAHLPT VEVAYGLTKN SLKMWKSGTT ATSDDYWLYT DGTVWNGVG VLGNNPETST GFEKITPNFN ASIKTYSASA TDGQTDFNIP FTFSTITVFV NGSIQLPGLN YTVSGSTLTF T TELEAGDL ...String:
MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSMETEGL TLDWNAHLPT VEVAYGLTKN SLKMWKSGTT ATSDDYWLYT DGTVWNGVG VLGNNPETST GFEKITPNFN ASIKTYSASA TDGQTDFNIP FTFSTITVFV NGSIQLPGLN YTVSGSTLTF T TELEAGDL LYVFIGNPNI STNDKLNRIY TANAMQGQTT IQVPYDFSTA IVYINGVLQN PITAYSIGAD RIITFSEELY QD DEIIIML GDIIIQSDEY VLKQELLDVN ASSYINTKSG NSIQEEFDIL YNSNSISKII YSDIKNINWD EINEIFVCGK TLN TTEGAG YFYYDNNDTI TVEDGGTCFV INNKRIKRRY IGPALSSWFT TIDGINTFLS TGNVSLRFDS NLTLTKALTI KSNT NLYFN KDVFLFPSGP TIQGLICSGS VSTTITTTLT SDVSSSSFIV NVTDASKFSV GDYVEIRSEK LVEGVNAQGV KIGIM RQIT KIDANQLYID KIALYDFTIS DNTLISKMDI VKNVNIDGLT FNNINYTTLF PITMNMVYCD NIVIKNTQLY GSKEKY TGD VSGRTALKIN SCRNVLIENC NAYHQGWYGV EILGYSEEVT VDKCFFDDCR HGVSINWSSI YGEPNGILIN DCTSTSS TL SGFDTHDIGR NITFSNCRAY KSGDDGFQIR ARNVKYINCL ADYSTLDGFG QGDGAINTRL IGCKATNNGR NGFSLVWE G GNIEDCEALN NQYGYAMLGG RIINSRGIDN SSACVDCGSN SDPANQFSLY IDNCDFPYST IQTRCLYFRG SSGIRPELV SVKNTNMAGY GNLWYLLGGY SSQPLSPMLN NNTLDINSTT APTSGMVTLT AGTATINTSA VKLSTSSTAS TLRYVSNIDL KRILSSSNI GTLSISNIVN GVSFTITSSN NLDASTIYWQ ISL

UniProtKB: Depolymerase, capsule K1-specific

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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

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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 / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4015926
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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