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Yorodumi- PDB-8x8o: Cryo-EM structure of a bacteriophage tail- spike protein against ... -
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-Basic information
Entry | Database: PDB / ID: 8x8o | ||||||
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Title | Cryo-EM structure of a bacteriophage tail- spike protein against Klebsiella pneumoniae K64,ORF41(K64-ORF41) in 5 mM EDTA | ||||||
Components | Probable tail spike protein | ||||||
Keywords | LYASE / K64-ORF41 / depolymerase / cryo-EM / Klebsiella pneumoniae K64 / capsule polysaccharide / EDTA | ||||||
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 | ||||||
Biological species | Klebsiella phage SH-Kp 152410 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||
Authors | Xie, Y. / Huang, T. / Zhang, Z. / Tao, X. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 8x8o.cif.gz | 409.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8x8o.ent.gz | 318.2 KB | Display | PDB format |
PDBx/mmJSON format | 8x8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8x8o_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8x8o_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8x8o_validation.xml.gz | 61.3 KB | Display | |
Data in CIF | 8x8o_validation.cif.gz | 95.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/8x8o ftp://data.pdbj.org/pub/pdb/validation_reports/x8/8x8o | HTTPS FTP |
-Related structure data
Related structure data | 38151MC 8x8mC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 112251.500 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella phage SH-Kp 152410 (virus) / Gene: 2410_orf00041 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K9VGS2 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: K64-ORF41 in 5 mM EDTA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Klebsiella phage SH-Kp 152410 (virus) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 371259 / Symmetry type: POINT | ||||||||||||||||||||||||
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