2JES

Portal protein (gp6) from bacteriophage SPP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.288 

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

  • 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.,Sect.D 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PORTAL PROTEIN
A, C, E, G, I, K, M, O, Q, S, U, W, Y
503Bacillus phage SPP1Mutation(s): 1 
Gene Names: 6 (siz)
Find proteins for P54309 (Bacillus phage SPP1)
Go to UniProtKB:  P54309
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN
B, D, F, H, J, L, N, P, R, T, V, X, Z
30N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O, Q, S, U, W, Y
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG

Download SDF File 
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
B, D, F, H, J, L, N, P, R, T, V, X, Z
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.288 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 174.314α = 90.00
b = 221.405β = 90.00
c = 421.866γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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