2JES

Portal protein (gp6) from bacteriophage SPP1

• PDB DOI:  https://doi.org/10.2210/pdb2JES/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bacillus phage SPP1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-01-21 Released: 2007-03-27 
• Deposition Author(s): 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.

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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 

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

• PubMed: 17363899 
• DOI: https://doi.org/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 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.

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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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C13  (3D View)
Global Stoichiometry: Hetero 26-mer - A13B13 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 782.82 kDa 
• Atom Count: 39,260 
• Modelled Residue Count: 5,200 
• Deposited Residue Count: 6,929 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PORTAL PROTEIN	A, C, E, G, I, K, M, O, Q, S, U, W, Y	503	Bacillus phage SPP1	Mutation(s): 1  Gene Names: 6, siz
UniProt
Find proteins for P54309 (Bacillus phage SPP1) Explore P54309  Go to UniProtKB:  P54309

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN	B, D, F, H, J, L, N, P, R, T, V, X, Z	30	Bacillus phage SPP1	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	AA [auth A], CA [auth C], EA [auth E], GA [auth G], IA [auth I], KA [auth K], MA [auth M], OA [auth O], QA [auth Q], SA [auth S], UA [auth U], WA [auth W], YA [auth Y]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
CA	BA [auth A], DA [auth C], FA [auth E], HA [auth G], JA [auth I], LA [auth K], NA [auth M], PA [auth O], RA [auth Q], TA [auth S], VA [auth U], XA [auth W], ZA [auth Y]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 174.314	α = 90
b = 221.405	β = 90
c = 421.866	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): 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.

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