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- EMDB-38149: Cryo-EM structure of a bacteriophage tail- spike protein against ... -

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Basic information

Entry
Database: EMDB / ID: EMD-38149
TitleCryo-EM structure of a bacteriophage tail- spike protein against Klebsiella pneumoniae K64,ORF41(K64-ORF41)
Map dataCryo-EM structure of a bacteriophage tail- spike protein against Klebsiella pneumoniae K64,ORF41(K64-ORF41)
Sample
  • Complex: K64-ORF41
    • Protein or peptide: Probable tail spike protein
KeywordsK64-ORF41 / depolymerase / cryo-EM / Klebsiella pneumoniae K64 / capsule polysaccharide / LYASE
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 / outer membrane / adhesion receptor-mediated virion attachment to host cell
Similarity search - Function
Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
Probable tail spike protein
Similarity search - Component
Biological speciesKlebsiella phage SH-Kp 152410 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsXie Y / Huang T / Zhang Z / Tao X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200803 China
CitationJournal: Int J Biol Macromol / Year: 2024
Title: Structural and functional basis of bacteriophage K64-ORF41 depolymerase for capsular polysaccharide degradation of Klebsiella pneumoniae K64.
Authors: Tianyun Huang / Zhuoyuan Zhang / Xin Tao / Xinyu Shi / Peng Lin / Dan Liao / Chenyu Ma / Xinle Cai / Wei Lin / Xiaofan Jiang / Peng Luo / Shan Wu / Yuan Xie /
Abstract: Capsule polysaccharide is an important virulence factor of Klebsiella pneumoniae (K. pneumoniae), which protects bacteria against the host immune response. A promising therapeutic approach is using ...Capsule polysaccharide is an important virulence factor of Klebsiella pneumoniae (K. pneumoniae), which protects bacteria against the host immune response. A promising therapeutic approach is using phage-derived depolymerases to degrade the capsular polysaccharide and expose and sensitize the bacteria to the host immune system. Here we determined the cryo-electron microscopy (cryo-EM) structures of a bacteriophage tail-spike protein against K. pneumoniae K64, ORF41 (K64-ORF41) and ORF41 in EDTA condition (K64-ORF41), at 2.37 Å and 2.50 Å resolution, respectively, for the first time. K64-ORF41 exists as a trimer and each protomer contains a β-helix domain including a right-handed parallel β-sheet helix fold capped at both ends, an insertion domain, and one β-sheet jellyroll domain. Moreover, our structural comparison with other depolymerases of K. pneumoniae suggests that the catalytic residues (Tyr528, His574 and Arg628) are highly conserved although the substrate of capsule polysaccharide is variable. Besides that, we figured out the important residues involved in the substrate binding pocket including Arg405, Tyr526, Trp550 and Phe669. This study establishes the structural and functional basis for the promising phage-derived broad-spectrum activity depolymerase therapeutics and effective CPS-degrading agents for the treatment of carbapenem-resistant K. pneumoniae K64 infections.
History
DepositionNov 27, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38149.png

Downloads & links

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Map

FileDownload / File: emd_38149.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of a bacteriophage tail- spike protein against Klebsiella pneumoniae K64,ORF41(K64-ORF41)
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: 0.011
Minimum - Maximum-0.03544836 - 0.08786519
Average (Standard dev.)0.000001298669 (±0.00347203)
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 ORF41(K64-ORF41)

Fileemd_38149_half_map_1.map
Annotationhalf1 map of ORF41(K64-ORF41)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2 map of ORF41(K64-ORF41)

Fileemd_38149_half_map_2.map
Annotationhalf2 map of ORF41(K64-ORF41)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : K64-ORF41

EntireName: K64-ORF41
Components
  • Complex: K64-ORF41
    • Protein or peptide: Probable tail spike protein

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Supramolecule #1: K64-ORF41

SupramoleculeName: K64-ORF41 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella phage SH-Kp 152410 (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 SH-Kp 152410 (virus)
Molecular weightTheoretical: 112.2515 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MDQDTKTIIQ YPTSGDEYDI PFDYLSRKFV RVSLVSNTQR VLLDNITDYR YVSRTRVKLL VSTDGYSRV EIRRFTSASE MVVDFSDGSV LRATDLNVSA LQSAHIAEEA RDLFSTSLSI GQLSYFDAKG LQIKNVAAGV D NTDAVTVQ ...String:
MGSSHHHHHH SSGLVPRGSH MDQDTKTIIQ YPTSGDEYDI PFDYLSRKFV RVSLVSNTQR VLLDNITDYR YVSRTRVKLL VSTDGYSRV EIRRFTSASE MVVDFSDGSV LRATDLNVSA LQSAHIAEEA RDLFSTSLSI GQLSYFDAKG LQIKNVAAGV D NTDAVTVQ QLNKIIADVV TTIPDSVADN IRGLWARVLG DIGITLVDGS FETGATITTR TQALWSISGR KCYTWAGALP KV VPENSTP ESTGGISETA WVDSSSKALG VLLAGPSGAE RVGLKQGGTV QDAINWLTFD SFDIVKDGSK DVTADIMAAC VVA NDLGLD IKQNDGTYLV SGNPVWPVYN SLDLNGVTLK LAAGFTGYFA LTQKDSTTVY GPTSPIVQAI NAAGGRTAGS GVLE GLVNS TELNGKFLFM EGADVLYYSR GTAKYWWTNT YLSNRGKLSD NLKYGVSAIT KITAVTPRTK IVYYRLPNLD FGNGP ANNG VIRVLNNTRF IMQGGSISNR PLKDVSKSPV IISLNYCAAF KAYDFFDPYP AFAVDSNNSL VYSYTLNFND IADAVF ENF NSQGYGWGVV GGQRSTNITY RDCNLNRVDM HNPYMGYLKV LDTRLGTWGI NASGMGDMYL ERVTVDLDDS AHGGHRE HE GIINARGDFG GFHDGGLYIK DLTIVGEASA FEATSGHPVA LVSAYSFNAS LAYIPESSPV TPWGFKEVIV EGLHCPFK R TGRRFNSIIS APSIQFTVYH PMRVKLEDCN FNSTAFEKFD LRGWRVTPYN PSKVGIANTL AFRPTNFVDV KDCSMVGLE FTRPTSAYDY SNFDVNLVNV KNVEEHSLSP FTLYTNQCGR YNLVGCGLQQ IVDKSMTSGE RANRRSTFSV TGGTWNSLSG NPTDITYGN GYDIPVVATG VMFVGPYSQT EVTGANLNVA EFVQASGCKF LSSGPTYIQP LLWSGAGGPT GASANFNVAR G NTLGLNIS AVNGETSQVI AATLVIPQGF STGPAAGTTY GFAVEKNINY QLGLNARSLK ANVGLVRCSD TITGVYLNA

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 TITAN
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

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 754113
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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