2JES

Portal protein (gp6) from bacteriophage SPP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.288 
  • R-Value Observed: 0.289 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Framework for DNA Translocation Via the Viral Portal Protein

Lebedev, A.A.Krause, M.H.Isidro, A.L.Vagin, A.A.Orlova, E.V.Turner, J.Dodson, E.J.Tavares, P.Antson, A.A.

(2007) EMBO J 26: 1984

  • DOI: 10.1038/sj.emboj.7601643
  • Primary Citation of Related Structures:  
    2JES

  • PubMed Abstract: 
  • Tailed bacteriophages and herpesviruses load their capsids with DNA through a tunnel formed by the portal protein assembly. Here we describe the X-ray structure of the bacteriophage SPP1 portal protein in its isolated 13-subunit form and the pseudoat ...

    Tailed bacteriophages and herpesviruses load their capsids with DNA through a tunnel formed by the portal protein assembly. Here we describe the X-ray structure of the bacteriophage SPP1 portal protein in its isolated 13-subunit form and the pseudoatomic structure of a 12-subunit assembly. The first defines the DNA-interacting segments (tunnel loops) that pack tightly against each other forming the most constricted part of the tunnel; the second shows that the functional dodecameric state must induce variability in the loop positions. Structural observations together with geometrical constraints dictate that in the portal-DNA complex, the loops form an undulating belt that fits and tightly embraces the helical DNA, suggesting that DNA translocation is accompanied by a 'mexican wave' of positional and conformational changes propagating sequentially along this belt.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Crystallographic Studies of the 13-Fold Symmetric Portal Protein of Bacteriophage Spp1
      Jekow, P., Schaper, S., Gunther, D., Tavares, P., Hinrichs, W.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 1008
    • Identification of a Gene in Bacillus Subtilis Bacteriophage Spp1 Determining the Amount of Packaged DNA
      Tavares, P., Santos, M.A., Lurz, R., Morelli, G., Delencastre, H., Trautner, T.A.
      (1992) J Mol Biol 225: 81

    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PORTAL PROTEINACEGIKMOQSUWY503Bacillus phage SPP1Mutation(s): 1 
Gene Names: 6siz
Find proteins for P54309 (Bacillus phage SPP1)
Explore P54309 
Go to UniProtKB:  P54309
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UNIDENTIFIED FRAGMENT OF PORTAL PROTEINBDFHJLNPRTVXZ30Bacillus phage SPP1Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download CCD File 
A, C, E, G, I, K, M, O, Q, S, U, W, Y
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, C, E, G, I, K, M, O, Q, S, U, W, Y
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.288 
  • R-Value Observed: 0.289 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.314α = 90
b = 221.405β = 90
c = 421.866γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-03-29
    Changes: Derived calculations, Structure summary