5VF3

Bacteriophage T4 isometric capsid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cryo-EM structure of the bacteriophage T4 isometric head at 3.3- angstrom resolution and its relevance to the assembly of icosahedral viruses.

Chen, Z.Sun, L.Zhang, Z.Fokine, A.Padilla-Sanchez, V.Hanein, D.Jiang, W.Rossmann, M.G.Rao, V.B.

(2017) Proc Natl Acad Sci U S A 114: E8184-E8193

  • DOI: 10.1073/pnas.1708483114
  • Primary Citation of Related Structures:  
    5VF3

  • PubMed Abstract: 
  • The 3.3-Å cryo-EM structure of the 860-Å-diameter isometric mutant bacteriophage T4 capsid has been determined. WT T4 has a prolate capsid characterized by triangulation numbers (T numbers) T end = 13 for end caps and T mid = 20 for midsection ...

    The 3.3-Å cryo-EM structure of the 860-Å-diameter isometric mutant bacteriophage T4 capsid has been determined. WT T4 has a prolate capsid characterized by triangulation numbers (T numbers) T end = 13 for end caps and T mid = 20 for midsection. A mutation in the major capsid protein, gp23, produced T=13 icosahedral capsids. The capsid is stabilized by 660 copies of the outer capsid protein, Soc, which clamp adjacent gp23 hexamers. The occupancies of Soc molecules are proportional to the size of the angle between the planes of adjacent hexameric capsomers. The angle between adjacent hexameric capsomers is greatest around the fivefold vertices, where there is the largest deviation from a planar hexagonal array. Thus, the Soc molecules reinforce the structure where there is the greatest strain in the gp23 hexagonal lattice. Mutations that change the angles between adjacent capsomers affect the positions of the pentameric vertices, resulting in different triangulation numbers in bacteriophage T4. The analysis of the T4 mutant head assembly gives guidance to how other icosahedral viruses reproducibly assemble into capsids with a predetermined T number, although the influence of scaffolding proteins is also important.


    Organizational Affiliation

    Department of Biology, The Catholic University of America, Washington, DC 20064; mr@purdue.edu rao@cua.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid vertex protein gp24A [auth a]417Escherichia virus T4Mutation(s): 0 
Gene Names: 24
UniProt
Find proteins for P19896 (Enterobacteria phage T4)
Explore P19896 
Go to UniProtKB:  P19896
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid protein456Escherichia virus T4Mutation(s): 0 
Gene Names: gp23
UniProt
Find proteins for P04535 (Enterobacteria phage T4)
Explore P04535 
Go to UniProtKB:  P04535
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small outer capsid protein80Escherichia virus T4Mutation(s): 0 
Gene Names: soc
UniProt
Find proteins for P03715 (Enterobacteria phage T4)
Explore P03715 
Go to UniProtKB:  P03715
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Highly immunogenic outer capsid proteinY [auth Z]376Escherichia virus T4Mutation(s): 0 
Gene Names: hoc
UniProt
Find proteins for P18056 (Enterobacteria phage T4)
Explore P18056 
Go to UniProtKB:  P18056
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Highly immunogenic outer capsid proteinZ [auth z]15Escherichia virus T4Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI081726
National Institutes of Health/Office of the DirectorUnited StatesS10 OD012372
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01 GM098412-S1

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2017-10-11
    Changes: Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence