5BU8

HK620 Tail Needle crystallized at pH 7.5 and derivatized with Xenon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions.

Bhardwaj, A.Sankhala, R.S.Olia, A.S.Brooke, D.Casjens, S.R.Taylor, D.J.Prevelige, P.E.Cingolani, G.

(2016) J Biol Chem 291: 215-226

  • DOI: 10.1074/jbc.M115.696260
  • Primary Citation of Related Structures:  
    4ZXQ, 5BU8, 5BU5, 5BVZ, 4ZKU, 4ZKP

  • PubMed Abstract: 
  • Bacterial viruses of the P22-like family encode a specialized tail needle essential for genome stabilization after DNA packaging and implicated in Gram-negative cell envelope penetration. The atomic structure of P22 tail needle (gp26) crystallized at acidic pH reveals a slender fiber containing an N-terminal "trimer of hairpins" tip ...

    Bacterial viruses of the P22-like family encode a specialized tail needle essential for genome stabilization after DNA packaging and implicated in Gram-negative cell envelope penetration. The atomic structure of P22 tail needle (gp26) crystallized at acidic pH reveals a slender fiber containing an N-terminal "trimer of hairpins" tip. Although the length and composition of tail needles vary significantly in Podoviridae, unexpectedly, the amino acid sequence of the N-terminal tip is exceptionally conserved in more than 200 genomes of P22-like phages and prophages. In this paper, we used x-ray crystallography and EM to investigate the neutral pH structure of three tail needles from bacteriophage P22, HK620, and Sf6. In all cases, we found that the N-terminal tip is poorly structured, in stark contrast to the compact trimer of hairpins seen in gp26 crystallized at acidic pH. Hydrogen-deuterium exchange mass spectrometry, limited proteolysis, circular dichroism spectroscopy, and gel filtration chromatography revealed that the N-terminal tip is highly dynamic in solution and unlikely to adopt a stable trimeric conformation at physiological pH. This is supported by the cryo-EM reconstruction of P22 mature virion tail, where the density of gp26 N-terminal tip is incompatible with a trimer of hairpins. We propose the tail needle N-terminal tip exists in two conformations: a pre-ejection extended conformation, which seals the portal vertex after genome packaging, and a postejection trimer of hairpins, which forms upon its release from the virion. The conformational plasticity of the tail needle N-terminal tip is built in the amino acid sequence, explaining its extraordinary conservation in nature.


    Organizational Affiliation

    From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, Italy gino.cingolani@jefferson.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA stabilization proteinA199Enterobacteria phage HK620Mutation(s): 0 
Gene Names: 26
UniProt
Find proteins for Q9AYZ3 (Enterobacteria phage HK620)
Explore Q9AYZ3 
Go to UniProtKB:  Q9AYZ3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA stabilization proteinB233Enterobacteria phage HK620Mutation(s): 0 
Gene Names: 26
UniProt
Find proteins for Q9AYZ3 (Enterobacteria phage HK620)
Explore Q9AYZ3 
Go to UniProtKB:  Q9AYZ3
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.231 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.642α = 90
b = 43.642β = 90
c = 271.063γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM100888

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-02
    Changes: Database references
  • Version 1.2: 2016-01-13
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2020-06-17
    Changes: Derived calculations