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- EMDB-32219: Cryo-EM structure of Depo32, a Klebsiella phage depolymerase targ... -

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Basic information

Entry
Database: EMDB / ID: EMD-32219
TitleCryo-EM structure of Depo32, a Klebsiella phage depolymerase targets the K2 serotype K. pneumoniae
Map data
Sample
  • Complex: Tail spike protein Depo32
    • Protein or peptide: Depolymerase
KeywordsDepolymerase / Klebsiella pneumoniae / K2 capsular type / Capsular polysaccharides / HYDROLASE
Function / homologybiological process involved in interaction with host / Pectin lyase fold/virulence factor / viral life cycle / virion component / Depolymerase
Function and homology information
Biological speciesKlebsiella phage 020009 (virus) / Klebsiella phage GH-K3 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsCai R / Ren Z
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32072824 China
National Natural Science Foundation of China (NSFC)31872505 China
National Natural Science Foundation of China (NSFC)U19A2038 China
CitationJournal: To Be Published
Title: Depo32, a depolymerase of Klebsiella phage, efficiently controls infection caused by Klebsiella pneumoniae with K2 serotype CPS
Authors: Cai R / Ren Z / Zhao R / Wang X / Guo Z / Du R / Han W / Ru H / Gu J
History
DepositionNov 15, 2021-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32219.png

Downloads & links

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Map

FileDownload / File: emd_32219.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.0139
Minimum - Maximum-0.08694031 - 0.19417128
Average (Standard dev.)0.0000059459176 (±0.0064281276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 278.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened by b-factor -50

Fileemd_32219_additional_1.map
Annotationsharpened by b-factor -50
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_32219_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_32219_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tail spike protein Depo32

EntireName: Tail spike protein Depo32
Components
  • Complex: Tail spike protein Depo32
    • Protein or peptide: Depolymerase

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Supramolecule #1: Tail spike protein Depo32

SupramoleculeName: Tail spike protein Depo32 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella phage 020009 (virus) / Strain: vB_KpnS_GH-K3
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Depolymerase

MacromoleculeName: Depolymerase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage GH-K3 (virus)
Molecular weightTheoretical: 100.947852 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MMALYREGKA AMAADGTVTG TGTKWQSSLS LIRPGATIMF LSSPIQMAVV NKVVSDTEIK AITTNGAVV ASTDYAILLS DSLTVDGLAQ DVAETLRYYQ SQETVIADAV EFFKEFDFES LQNLANQIKA DSEASESSAA A AAASESKA ...String:
MGSSHHHHHH SSGLVPRGSH MMALYREGKA AMAADGTVTG TGTKWQSSLS LIRPGATIMF LSSPIQMAVV NKVVSDTEIK AITTNGAVV ASTDYAILLS DSLTVDGLAQ DVAETLRYYQ SQETVIADAV EFFKEFDFES LQNLANQIKA DSEASESSAA A AAASESKA KTSEDNAKSS ENAAKNSEVA AETTRDQIQQ IIDNAGDQST LVVLAQPDGF DSIGRVSSFA ALRNLKPKKS GQ HVLLTSY YDGWAAENKM PTGGGEFISS IGTATDDGGY IAAGPGYYWT RVVNNNSFTA EDFGCKTTAT PPPNFNVLPA ELF DNTARM QAAFNLAISK SFKLNLSAGT YYFESSDTLR ITGPIHIEGR PGTVFYHNPS NKANPKTDAF MNISGCSMGR ISSI NCFSN SYLGKGINFD RSVGDNRKLV LEHVYVDTFR WGFYVGEPEC INQIEFHSCR AQSNYFQGIF IESFKEGQEY GHSAP VHFF NTICNGNGPT SFALGATYKT TKNEYIKVMD SVNDVGCQAY FQGLSNVQYI GGQLSGHGSP RNTSLATITQ CNSFII YGT DLEDINGFTT DGTAITADNI DTIESNYLKD ISGAAIVVSS CLGFKIDSPH IFKIKTLSTI KLMNNTYNYE IGGFTPD EA LKYNVWDANG LATNRISGVI HPRLVNSRLG INSVAFDNMS NKLDVSSLIH NETSQIIGLT PSTGSNVPHT RIMWSNGA M YSSTDLNNGF RLNYLSNHNE PLTPMHLYNE FSVSEFGGSV TESNALDEIK YIFIQTTYAN SGDGRFIIQA LDASGSVLS SNWYSPQSFN STFPISGFVR FDVPTGAKKI RYGFVNSANY TGSLRSHFMS GFAYNKRFFL KIYAVYNDLG RYGQFEPPYS VAIDRFRVG DNTTQMPSIP ASSATDVAGV NEVINSLLAS LKANGFMSS

UniProtKB: Depolymerase

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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

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMNH2C(CH2OH)3tris(hydroxymethyl)aminomethane
150.0 mMNaClSodium chloridesodium chloride
0.5 mMC9H15O6Ptris(2-carboxyethyl)phosphine
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot 3.5 or 4 seconds before plunging.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.56 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 462388
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL
Output model

PDB-7vz3:
Cryo-EM structure of Depo32, a Klebsiella phage depolymerase targets the K2 serotype K. pneumoniae

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