+Open data
-Basic information
Entry | Database: PDB / ID: 8xck | |||||||||
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Title | Closed state of central tail fiber of bacteriophage lambda | |||||||||
Components |
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Keywords | VIRUS / Bacteriophage / caudovirales / siphoviridae / phage lambda / host recognition / LamB / cryo-EM | |||||||||
Function / homology | Function and homology information symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / outer membrane-bounded periplasmic space / host cell cytoplasm / periplasmic space / entry receptor-mediated virion attachment to host cell ...symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / outer membrane-bounded periplasmic space / host cell cytoplasm / periplasmic space / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / virion attachment to host cell Similarity search - Function | |||||||||
Biological species | Escherichia phage Lambda (virus) Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å | |||||||||
Authors | Ge, X.F. / Wang, J.W. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural mechanism of bacteriophage lambda tail's interaction with the bacterial receptor. Authors: Xiaofei Ge / Jiawei Wang / Abstract: Bacteriophage infection, a pivotal process in microbiology, initiates with the phage's tail recognizing and binding to the bacterial cell surface, which then mediates the injection of viral DNA. ...Bacteriophage infection, a pivotal process in microbiology, initiates with the phage's tail recognizing and binding to the bacterial cell surface, which then mediates the injection of viral DNA. Although comprehensive studies on the interaction between bacteriophage lambda and its outer membrane receptor, LamB, have provided rich information about the system's biochemical properties, the precise molecular mechanism remains undetermined. This study revealed the high-resolution cryo-electron microscopy (cryo-EM) structures of the bacteriophage lambda tail complexed with its irreversible Shigella sonnei 3070 LamB receptor and the closed central tail fiber. These structures reveal the complex processes that trigger infection and demonstrate a substantial conformational change in the phage lambda tail tip upon LamB binding. Providing detailed structures of bacteriophage lambda infection initiation, this study contributes to the expanding knowledge of lambda-bacterial interaction, which holds significance in the fields of microbiology and therapeutic development. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xck.cif.gz | 278.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xck.ent.gz | 220.5 KB | Display | PDB format |
PDBx/mmJSON format | 8xck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xck_validation.pdf.gz | 1019.2 KB | Display | wwPDB validaton report |
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Full document | 8xck_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8xck_validation.xml.gz | 57.3 KB | Display | |
Data in CIF | 8xck_validation.cif.gz | 86 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/8xck ftp://data.pdbj.org/pub/pdb/validation_reports/xc/8xck | HTTPS FTP |
-Related structure data
Related structure data | 38246MC 8xcgC 8xciC 8xcjC 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: 46045.844 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage Lambda (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P03749 #2: Protein | Mass: 20453.277 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ppiA, rot, rotA, b3363, JW3326 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFL3, peptidylprolyl isomerase |
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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
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 7 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 369942 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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