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- EMDB-63624: Cryo-EM structure of Dp42 depolymerase with C3 symmetry against K... -

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Basic information

Entry
Database: EMDB / ID: EMD-63624
TitleCryo-EM structure of Dp42 depolymerase with C3 symmetry against KN1 serotype Klebsiella pneumoniae,(Dp42-C3)
Map dataDp42 with C3 symmetry
Sample
  • Complex: Dp42 with C3 symmetry (Dp42-C3)
    • Protein or peptide: Probable tail spike protein
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 / Probable tail spike protein
Function and homology information
Biological speciesKlebsiella phage vB_KpnP_IME321 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 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_63624.png

Downloads & links

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Map

FileDownload / File: emd_63624.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDp42 with C3 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 250 pix.
= 212.75 Å		0.85 Å/pix.
x 250 pix.
= 212.75 Å		0.85 Å/pix.
x 250 pix.
= 212.75 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: 0.00582
Minimum - Maximum-0.018120997 - 0.039959863
Average (Standard dev.)0.0000036027127 (±0.0017230492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 212.75 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM half1 map of Dp42 with C3 symmetry

Fileemd_63624_half_map_1.map
AnnotationEM half1 map of Dp42 with C3 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half2 map of Dp42 with C3 symmetry

Fileemd_63624_half_map_2.map
AnnotationEM half2 map of Dp42 with C3 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dp42 with C3 symmetry (Dp42-C3)

EntireName: Dp42 with C3 symmetry (Dp42-C3)
Components
  • Complex: Dp42 with C3 symmetry (Dp42-C3)
    • Protein or peptide: Probable tail spike protein

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Supramolecule #1: Dp42 with C3 symmetry (Dp42-C3)

SupramoleculeName: Dp42 with C3 symmetry (Dp42-C3) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella phage vB_KpnP_IME321 (virus)

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Macromolecule #1: Probable tail spike protein

MacromoleculeName: Probable tail spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage vB_KpnP_IME321 (virus)
Molecular weightTheoretical: 92.402719 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MNQDIKTIIQ YPVGDVEFDI PFDYLSRKFV RVYLVSPLNR RQLNNITEYR YVSRTRIKLL VETAGFNLI EIRRFTSASE RVVDFSDGSV LRAADLNVSQ LQSAHIAEEA RDAAMLTISP ADDGSLDASG KVIKNVGTPV Q SSDAATKG ...String:
MGSSHHHHHH SSGLVPRGSH MNQDIKTIIQ YPVGDVEFDI PFDYLSRKFV RVYLVSPLNR RQLNNITEYR YVSRTRIKLL VETAGFNLI EIRRFTSASE RVVDFSDGSV LRAADLNVSQ LQSAHIAEEA RDAAMLTISP ADDGSLDASG KVIKNVGTPV Q SSDAATKG YVDTTVAPLA TTIEANFMRT LRTSGRSIRE LPGASEVAGM LLGFNGEGDP VPVVAGEGTA SDVMLKLAGT TG LSYIGGV GYVTPEMMTV DGKTLVRGLG QDHVRFIQKA IDEGHRRNVP VLLSGGGYEV YETLHDAPLP RDDGTAYPEW VAN GGDSNI RPEEQLYQKA HLRLYNNSVI LGAGSQITTI RSTWSRGTSA VDLTSPIMWY IEGPLGNRGT VSYVLKGIKT MGAY IGRYV VGISYRSIED DLEFSGCGIS GVKQGEEQTL HRKIVITAYA GDVTGGWWLQ RNNAYGTKYM PPYTDTDVWL MGWCD SSKY EYLSYTGYDY YGRDALVHDW ISEWFDTYIF KSANSRKVSE GGRLTNQSAN PYPLPTLKGI TGRARYITSR YSRQNA LNI IDTLKTLITI RAPGYMDNST QSCRIVNAMI EAVGLIRRTS GANAGNYFGI DVVDKWGADT GVWGLEGTGI LEQQLVV FL RPGVPCTNAV VATGAGQIFE SWTTTNAQRR LLALRDWNPA TQVQTYRYDF RTDYALMRPT RYYTDGPLWN YSKGTSTP T VAVNGSAIAV QKAVSNWYRL GDIMRCNIYV EINSITLQGN SELTVTTPSY NGSWEVAGQG IGKVYLSTLT GDVTLTPVI QQGSNVVRLR RGSSPEVYTF AAGTYNNVVL IIGIDYVPAS

UniProtKB: Probable tail spike protein

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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: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 325681
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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