[English] 日本語
Yorodumi- PDB-8xci: Open state of central tail fiber of bacteriophage lambda upon bin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xci | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Open state of central tail fiber of bacteriophage lambda upon binding to LamB | |||||||||
Components | Tip attachment protein J | |||||||||
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 / host cell cytoplasm / 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) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å | |||||||||
Authors | Ge, X.F. / Wang, J.W. | |||||||||
Funding support | China, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8xci.cif.gz | 270.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8xci.ent.gz | 194 KB | Display | PDB format |
PDBx/mmJSON format | 8xci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xci_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8xci_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8xci_validation.xml.gz | 58.4 KB | Display | |
Data in CIF | 8xci_validation.cif.gz | 84.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/8xci ftp://data.pdbj.org/pub/pdb/validation_reports/xc/8xci | HTTPS FTP |
-Related structure data
Related structure data | 38244MC 8xcgC 8xcjC 8xckC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 124550.625 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 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Bacteriophage lambda tail with LamB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Escherichia phage Lambda (virus) |
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 |
---|---|
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 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 358235 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|