6QWP

Crystal structure of T7 bacteriophage portal protein, 13mer, closed valve


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism.

Cuervo, A.Fabrega-Ferrer, M.Machon, C.Conesa, J.J.Fernandez, F.J.Perez-Luque, R.Perez-Ruiz, M.Pous, J.Vega, M.C.Carrascosa, J.L.Coll, M.

(2019) Nat Commun 10: 3746-3746

  • DOI: https://doi.org/10.1038/s41467-019-11705-9
  • Primary Citation of Related Structures:  
    6QWP, 6QX5, 6QXM, 6R21

  • PubMed Abstract: 

    Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been packaged, the tail components assemble on the portal to render the mature infective virion. The tail tightly seals the ejection conduit until infection, when its interaction with the host membrane triggers the opening of the channel and the viral genome is delivered to the host cell. Using high-resolution cryo-electron microscopy and X-ray crystallography, here we describe various structures of the T7 bacteriophage portal and fiber-less tail complex, which suggest a possible mechanism for DNA retention and ejection: a portal closed conformation temporarily retains the genome before the tail is assembled, whereas an open portal is found in the tail. Moreover, a fold including a seven-bladed β-propeller domain is described for the nozzle tail protein.


  • Organizational Affiliation

    Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M
547Escherichia phage T7Mutation(s): 0 
UniProt
Find proteins for P03728 (Escherichia phage T7)
Explore P03728 
Go to UniProtKB:  P03728
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03728
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 261.57α = 90
b = 261.57β = 90
c = 256.07γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU 2014-54181
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU2014-53550-P
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU2017-83720-P
Spanish Ministry of Science, Innovation, and UniversitiesSpainMDM-2014-0435
Spanish Ministry of Science, Innovation, and UniversitiesSpainSEV-2013-0347
Spanish Ministry of Science, Innovation, and UniversitiesSpainRYC-2011-09071
European Commission653706

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references, Refinement description