5VF3 Virus date Apr 06, 2017
title Bacteriophage T4 Isometric Capsid
authors Z.Chen, L.Sun, Z.Zhang, A.Fokine, V.Padilla-Sanchez, D.Hanein, W.J M.G.Rossmann, V.B.Rao
compound source
Molecule: Capsid Vertex Protein Gp24
Chain: a
Synonym: Gene Product 24, Gp24, Gp24
 Organism_scientific: Enterobacteria Phage T4
Organism_taxid: 10665

Molecule: Major Capsid Protein
Chain: A, B, C, D, E, F, G, H, I, J, K, L
Synonym: Gene Product 23, Gp23, Major Head Protein, Gp23
Organism_scientific: Enterobacteria Phage T4
Organism_taxid: 10665

Molecule: Small Outer Capsid Protein
Chain: O, P, Q, R, S, T, U, V, W, X, Y
Synonym: Soc
Organism_scientific: Enterobacteria Phage T4
Organism_taxid: 10665

Molecule: Highly Immunogenic Outer Capsid Protein
Chain: Z
Synonym: Hoc
Organism_scientific: Enterobacteria Phage T4
Organism_taxid: 10665

Molecule: Highly Immunogenic Outer Capsid Protein
Chain: z
Fragment: Unidentified Segment
Synonym: Hoc
Organism_scientific: Enterobacteria Phage T4
Organism_taxid: 10665
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.30 Å
Gene
Ontology
ChainFunctionProcessComponent
S, O, W, T, X, P, Y, V, Q, R, U


Z


a


Primary referenceCryo-EM structure of the bacteriophage T4 isometric head at 3.3-A 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 MG, Rao VB, Proc Natl Acad Sci U S A. 2017 Sep 11. pii: 201708483. doi:, 10.1073/pnas.1708483114. PMID:28893988
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1032 Kb) [Save to disk]
  • Biological Unit Coordinates (5vf3.pdb1.gz) 60774 Kb
  • CSU: Contacts of Structural Units for 5VF3
  • Retrieve 5VF3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VF3 from S2C, [Save to disk]
    • View 5VF3 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5VF3
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vf3_a] [5vf3_I] [5vf3_K] [5vf3_C] [5vf3_O] [5vf3_V] [5vf3_B] [5vf3_L] [5vf3_Q] [5vf3_W] [5vf3_G] [5vf3_z] [5vf3_A] [5vf3_T] [5vf3_J] [5vf3_R] [5vf3_F] [5vf3_E] [5vf3_D] [5vf3_Z] [5vf3_S] [5vf3_U] [5vf3_Y] [5vf3_H] [5vf3_X] [5vf3_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5VF3
  • Community annotation for 5VF3 at PDBWiki (http://pdbwiki.org)

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