6UZC | pdb_00006uzc

Portal vertex structure of bacteriophage T4

  • Classification: VIRUS
  • Organism(s): Tequatrovirus T4
  • Mutation(s): No 

  • Deposited: 2019-11-14 Released: 2020-04-29 
  • Deposition Author(s): Fang, Q., Fokine, A., Rao, V.B.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6UZC

This is version 1.2 of the entry. See complete history

Literature

Structural morphing in a symmetry-mismatched viral vertex.

Fang, Q.Tang, W.C.Tao, P.Mahalingam, M.Fokine, A.Rossmann, M.G.Rao, V.B.

(2020) Nat Commun 11: 1713-1713

  • DOI: https://doi.org/10.1038/s41467-020-15575-4
  • Primary Citation Related Structures: 
    6UZC

  • PubMed Abstract: 

    Large biological structures are assembled from smaller, often symmetric, sub-structures. However, asymmetry among sub-structures is fundamentally important for biological function. An extreme form of asymmetry, a 12-fold-symmetric dodecameric portal complex inserted into a 5-fold-symmetric capsid vertex, is found in numerous icosahedral viruses, including tailed bacteriophages, herpesviruses, and archaeal viruses. This vertex is critical for driving capsid assembly, DNA packaging, tail attachment, and genome ejection. Here, we report the near-atomic in situ structure of the symmetry-mismatched portal vertex from bacteriophage T4. Remarkably, the local structure of portal morphs to compensate for symmetry-mismatch, forming similar interactions in different capsid environments while maintaining strict symmetry in the rest of the structure. This creates a unique and unusually dynamic symmetry-mismatched vertex that is central to building an infectious virion.


  • Organizational Affiliation
    • Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.

Macromolecule Content 

  • Total Structure Weight: 2,415.63 kDa 
  • Atom Count: 150,312 
  • Modeled Residue Count: 19,473 
  • Deposited Residue Count: 21,918 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Major capsid protein521Tequatrovirus T4Mutation(s): 0 
UniProt
Find proteins for P04535 (Enterobacteria phage T4)
Explore P04535 
Go to UniProtKB:  P04535
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04535
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Portal protein524Tequatrovirus T4Mutation(s): 0 
UniProt
Find proteins for P13334 (Enterobacteria phage T4)
Explore P13334 
Go to UniProtKB:  P13334
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13334
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI081726

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references