5NGJ

Crystal structure of pb6, major tail tube protein of bacteriophage T5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection.

Arnaud, C.A.Effantin, G.Vives, C.Engilberge, S.Bacia, M.Boulanger, P.Girard, E.Schoehn, G.Breyton, C.

(2017) Nat Commun 8: 1953-1953

  • DOI: 10.1038/s41467-017-02049-3

  • PubMed Abstract: 
  • The vast majority of phages, bacterial viruses, possess a tail ensuring host recognition, cell wall perforation and safe viral DNA transfer from the capsid to the host cytoplasm. Long flexible tails are formed from the tail tube protein (TTP) polymer ...

    The vast majority of phages, bacterial viruses, possess a tail ensuring host recognition, cell wall perforation and safe viral DNA transfer from the capsid to the host cytoplasm. Long flexible tails are formed from the tail tube protein (TTP) polymerised as hexameric rings around and stacked along the tape measure protein (TMP). Here, we report the crystal structure of T5 TTP pb6 at 2.2 Å resolution. Pb6 is unusual in forming a trimeric ring, although structure analysis reveals homology with all classical TTPs and related tube proteins of bacterial puncturing devices (type VI secretion system and R-pyocin). Structures of T5 tail tubes before and after interaction with the host receptor were determined by cryo-electron microscopy at 6 Å resolution. Comparison of these two structures reveals that host-binding information is not propagated to the capsid through conformational changes in the tail tube, suggesting a role of the TMP in this information transduction process.


    Organizational Affiliation

    Université Grenoble Alpes, CNRS, CEA, Institut for Structural Biology (IBS), 38000, Grenoble, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Gif-sur-Yvette, France.,Université Grenoble Alpes, CNRS, CEA, Institut for Structural Biology (IBS), 38000, Grenoble, France. Cecile.Breyton@ibs.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tail tube protein
A, B
477Escherichia phage T5Mutation(s): 0 
Gene Names: N4
Find proteins for Q6QGE2 (Escherichia phage T5)
Go to UniProtKB:  Q6QGE2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 76.790α = 90.00
b = 115.081β = 111.88
c = 83.366γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
XDSdata reduction
SCALAdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-INSB-05-02
LABEX GRALFranceANR-10-LABX-49-01

Revision History 

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2019-10-16
    Type: Data collection