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- EMDB-63622: KN1dep depolymerase with C1 symmetry against KN1 serotype Klebsie... -

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Basic information

Entry
Database: EMDB / ID: EMD-63622
TitleKN1dep depolymerase with C1 symmetry against KN1 serotype Klebsiella pneumoniae,(KN1dep-C1)
Map dataCryo-EM structure of KN1dep depolymerase with C1 symmetry against KN1 serotype Klebsiella pneumoniae,(KN1dep-C1)
Sample
  • Complex: KN1dep with C1 symmetry (KN1dep-C1)
    • Protein or peptide: Depolymerase, capsule KN1-specific
KeywordsDp42 / depolymerase / cryo-EM / Klebsiella pneumoniae KN1 / capsule polysaccharide LYASE / LYASE
Function / homologysymbiont entry into host cell via disruption of host cell glycocalyx / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein, N-terminal domain / symbiont entry into host cell via disruption of host cell envelope / virus tail / adhesion receptor-mediated virion attachment to host cell / Depolymerase, capsule KN1-specific
Function and homology information
Biological speciesKlebsiella phage vB_KpnP_IME321 (virus) / Klebsiella phage KN1-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsXie Y / Huang T / Shi X / Tao X / Ma C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200803 China
CitationJournal: To Be Published
Title: Structures and the mechanism investigation of bacteriophage depolymerases for capsular polysaccharide degradation of Klebsiella pneumoniae KN1 serotype
Authors: Xie Y
History
DepositionMar 4, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63622.png

Downloads & links

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Map

FileDownload / File: emd_63622.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of KN1dep depolymerase with C1 symmetry against KN1 serotype Klebsiella pneumoniae,(KN1dep-C1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 270 pix.
= 229.77 Å		0.85 Å/pix.
x 270 pix.
= 229.77 Å		0.85 Å/pix.
x 270 pix.
= 229.77 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.851 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0157
Minimum - Maximum-0.046793785 - 0.10312339
Average (Standard dev.)-0.000009262638 (±0.0043744836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 229.77 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half1 map of KN1dep depolymerase

Fileemd_63622_half_map_1.map
Annotationhalf1 map of KN1dep depolymerase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2 map of KN1dep depolymerase

Fileemd_63622_half_map_2.map
Annotationhalf2 map of KN1dep depolymerase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : KN1dep with C1 symmetry (KN1dep-C1)

EntireName: KN1dep with C1 symmetry (KN1dep-C1)
Components
  • Complex: KN1dep with C1 symmetry (KN1dep-C1)
    • Protein or peptide: Depolymerase, capsule KN1-specific

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Supramolecule #1: KN1dep with C1 symmetry (KN1dep-C1)

SupramoleculeName: KN1dep with C1 symmetry (KN1dep-C1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella phage vB_KpnP_IME321 (virus)

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Macromolecule #1: Depolymerase, capsule KN1-specific

MacromoleculeName: Depolymerase, capsule KN1-specific / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KN1-1 (virus)
Molecular weightTheoretical: 92.291773 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MMNQDIKTII QYPVGDVEFD IPFDYLSRKF VRVYLVSPLN RRQLNNITEY RYVSRTRIKL LVETAGFNL IEIRRFTSAS ERVVDFSDGS VLRATDLNVS QLQSAHIAEE ARDAAMLTIS PADDGSLDAS GKVIKNVGTP V QSSDAATK ...String:
MGSSHHHHHH SSGLVPRGSH MMNQDIKTII QYPVGDVEFD IPFDYLSRKF VRVYLVSPLN RRQLNNITEY RYVSRTRIKL LVETAGFNL IEIRRFTSAS ERVVDFSDGS VLRATDLNVS QLQSAHIAEE ARDAAMLTIS PADDGSLDAS GKVIKNVGTP V QSSDAATK GYVDTAVSPL ATTIEANFMR TLRTSGRSIR ELPGASEVAG MLLGFNGEGD PVPVVAGEGT ASDVMLKLAG TT GLSYIGG VGYVTPEMMT VDGKTLVRGL GQDHVRFIQK AIDEGHRRNV PVILSGGYEV YETLHDAPLP RDDGTAYPEW VAN GGDSNI RPEEQLYQKA HLRLYNNSVI LGAGSQIATI RSTWARSTSA VGLTSPIMWY IEGPLGNRGT VSYVLKGIKT IGAY IGRYV VGISYRSVED DLEFAGCGIA GVKQGEEQTI HRKIVITAYA GDVTGGWWLQ RNNAYGAKYM PPYTDTDVWL LGWCD SSTY EYLSYTGYDY DGRDALVHDW ISEWFDTYIF KTANSRKVSE GGRLTYQSAN PYPLPTLKGI TGRARYITSR YSRQNA LNV INTLKTLITI RAPGYMDNST QSCRILNAMI ESVGLIRRTS GANAGNYFGI DVVDKWGADT GVWGLEGTGI LEKQLVV FL RPGVPCTNAV VATGAGQIFE SWTTTNAQRR LLALRDWNPA TQVQTYRYDF RTDYALMRPT RYYTDGPLWN YSKGTSTP T VAVNGSTIAV QKAVTNWYRL GDIMRCNIYV EINSITLQGN SELTVTTPSF NGSWEVAGQG IGKVYLSTLT GGVTLTPVI QQGGNVVRLR KGSSPEVYAF EAGTYNNVVL IIGIDYVPLS

UniProtKB: Depolymerase, capsule KN1-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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162647
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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