[English] 日本語
Yorodumi- PDB-6p3e: Mobile loops and electrostatic interactions maintain the flexible... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p3e | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Mobile loops and electrostatic interactions maintain the flexible lambda tail tube | |||||||||
Components | Tail tube protein | |||||||||
Keywords | VIRAL PROTEIN / Tail tube / siphoviridae / helical | |||||||||
Function / homology | Function and homology information virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / host cell cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia phage lambda (virus) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5.4 Å | |||||||||
Authors | Campbell, P. / Duda, R.L. / Nassur, J. / Hendrix, R.W. / Conway, J.F. / Huet, A. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: J Mol Biol / Year: 2020 Title: Mobile Loops and Electrostatic Interactions Maintain the Flexible Tail Tube of Bacteriophage Lambda. Authors: Patricia L Campbell / Robert L Duda / Jamie Nassur / James F Conway / Alexis Huet / Abstract: The long flexible tail tube of bacteriophage lambda connects its capsid to the tail tip. On infection, a DNA ejection signal is passed from the tip, along the tube to the capsid that triggers passage ...The long flexible tail tube of bacteriophage lambda connects its capsid to the tail tip. On infection, a DNA ejection signal is passed from the tip, along the tube to the capsid that triggers passage of the DNA down the tube and into the host bacterium. The tail tube is built from repeating units of the major tail protein, gpV, which has two distinctive domains. Its N-terminal domain has the same fold as proteins that form the rigid inner tubes of contractile tail phages, such as T4, and its C-terminal domain adopt an Ig-like fold of unknown function. We determined structures of the lambda tail tube in free tails and in virions before and after DNA ejection using cryoelectron microscopy. Modeling of the density maps reveals how electrostatic interactions and a mobile loop participate in assembly and also impart flexibility to the tube while maintaining its integrity. We also demonstrate how a common protein fold produces rigid tubes in some phages but flexible tubes in others. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6p3e.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6p3e.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6p3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p3e_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6p3e_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6p3e_validation.xml.gz | 175.4 KB | Display | |
Data in CIF | 6p3e_validation.cif.gz | 212.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/6p3e ftp://data.pdbj.org/pub/pdb/validation_reports/p3/6p3e | HTTPS FTP |
-Related structure data
Related structure data | 20241MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
Symmetry | Helical symmetry: (Circular symmetry: 6 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 5 / Rise per n subunits: 42.8 Å / Rotation per n subunits: 17.5 °) |
-Components
#1: Protein | Mass: 25831.779 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: V, lambdap13 / Production host: Escherichia coli (E. coli) / References: UniProt: P03733 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: tail tube of the lambda phage / Type: COMPLEX / Details: plasmid expression of the tail genes / Entity ID: all / Source: RECOMBINANT | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 37 kDa/nm / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Escherichia phage lambda (virus) | ||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE | ||||||||||||
Natural host | Organism: Escherichia coli | ||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||
Buffer component |
| ||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: purified tail | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1240 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 17.5 ° / Axial rise/subunit: 42.8 Å / Axial symmetry: C6 | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 7934 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5543 / Num. of class averages: 1 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 200 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Pdb chain-ID: A / Source name: PDB / Type: experimental model
|