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PDBsum entry 3c9i

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protein metals Protein-protein interface(s) links
Viral protein PDB id
3c9i
Jmol
Contents
Protein chains
233 a.a. *
221 a.a. *
Metals
_CL ×2
_XE ×14
_CA ×2
Waters ×1590
* Residue conservation analysis
PDB id:
3c9i
Name: Viral protein
Title: Structure of p22 tail-needle gp26 bound to xenon gas
Structure: Tail needle protein gp26. Chain: a, b, c, d, e, f. Synonym: packaged DNA stabilization protein. Engineered: yes. Mutation: yes
Source: Bacteriophage p22. Gene: 26. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.95Å     R-factor:   0.234     R-free:   0.269
Authors: G.Cingolani,A.S.Olia
Key ref:
A.S.Olia et al. (2009). Structural plasticity of the phage P22 tail needle gp26 probed with xenon gas. Protein Sci, 18, 537-548. PubMed id: 19241380 DOI: 10.1002/pro.53
Date:
15-Feb-08     Release date:   03-Mar-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P35837  (VG26_BPP22) -  Tail needle protein gp26
Seq:
Struc:
233 a.a.
233 a.a.*
Protein chains
Pfam  
P35837  (VG26_BPP22) -  Tail needle protein gp26
Seq:
Struc:
233 a.a.
221 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     virion   1 term 
  Biological process     ?   2 terms 

 

 
DOI no: 10.1002/pro.53 Protein Sci 18:537-548 (2009)
PubMed id: 19241380  
 
 
Structural plasticity of the phage P22 tail needle gp26 probed with xenon gas.
A.S.Olia, S.Casjens, G.Cingolani.
 
  ABSTRACT  
 
The tail needle, gp26, is a highly stable homo-trimeric fiber found in the tail apparatus of bacteriophage P22. In the mature virion, gp26 is responsible for plugging the DNA exit channel, and likely plays an important role in penetrating the host cell envelope. In this article, we have determined the 1.98 A resolution crystal structure of gp26 bound to xenon gas. The structure led us to identify a calcium and a chloride ion intimately bound at the interior of alpha-helical core, as well as seven small cavities occupied by xenon atoms. The two ions engage in buried polar interactions with gp26 side chains that provide specificity and register to gp26 helical core, thus enhancing its stability. Conversely, the distribution of xenon accessible cavities correlates well with the flexibility of the fiber observed in solution and in the crystal structure. We suggest that small internal cavities in gp26 between the helical core and the C-terminal tip allow for flexible swinging of the latter, without affecting the overall stability of the protein. The C-terminal tip may be important in scanning the bacterial surface in search of a cell-envelope penetration site, or for recognition of a yet unidentified receptor on the surface of the host.
 
  Selected figure(s)  
 
Figure 1.
Three-dimensional structure of phage P22 tail needle bound to xenon gas. (a) Worm representation of tail needle gp26 bound to seven xenon atoms, one calcium, and one chloride atom (represented as green, gold, orange spheres, respectively). The structure was determined to 1.98 A resolution and refined to an R[free] of 26.8% (Table I). The tail needle is [similar]240 A homotrimer, consisting of four structural domains (indicated by horizontal arrows). All xenon and chloride atoms were found in cavities at the gp26 internal trimerization interface. (b --d) Close-up view of the three classes of xenon sites observed inside gp26 core: the orientation of gp26 shown is perpendicular to that in (a). Gp26 residues lining the binding site are depicted as ball-and-sticks with nitrogen and oxygen atoms colored in blue and red, respectively. Only residues of protomer A of gp26 are labeled. The blue and red densities around xenon atoms represent anomalous difference maps computed using X-ray data measured at low energy ([lambda] = 1.75 A) and high energy ([lambda] = 0.95 A), respectively (datasets Xe-Low and Xe-High in Table I). All anomalous maps were computed to 2.5 A resolution and contoured at 15[sigma] above background. The refined B-factor to 1.98 A resolution for xenon atoms Xe2, Xe3, Xe5, and Xe6 ranges between 32 and 39 A^2, whereas Xe1, Xe4, and Xe7 have significantly higher B-factor, between 60 and 96 A^2 (Table I).
Figure 2.
Ions trapped at the interior of gp26 trimerization interface. (a) Worm representation of tail needle gp26, with the calcium and chlorine ions displayed as a gold sphere and orange sphere, respectively. (b) Sequence alignment of the putative tail needle sequence from 12 P22-like phages. For simplicity, only the amino sequence spanning residues 60 --103 is displayed. Invariant residues interacting with the two ions are highlighted in dark pink, and partially conserved interacting residues in light pink. Other conserved residues are indicated below the alignment, where an asterisk (*) indicates an invariant residue, and a colon (:) a highly conserved residue. (c, d) Close-up view of the calcium and chloride ions observed at the gp26 internal trimerization interface. In both panels, the green density around the ions represents a F[Obs] [minus sign] F[Cal] difference map computed using structure factor amplitudes from the final refined model missing the Ca1 and Cl1 ions. The density was computed to 2.5 A and contoured at 5[sigma]. The calcium site has a refined B-factor of [similar]21 A^2 and the chlorine site [similar]28 A^2, respectively. The blue density around the ions represents an anomalous map computed using anomalous differences measured at low energy ([lambda] = 1.75 A, dataset Xe-Low in Table I) and contoured at 2[sigma].
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2009, 18, 537-548) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21499245 A.S.Olia, P.E.Prevelige, J.E.Johnson, and G.Cingolani (2011).
Three-dimensional structure of a viral genome-delivery portal vertex.
  Nat Struct Mol Biol, 18, 597-603.
PDB codes: 1vt0 3lj4 3lj5
20490881 J.A.Tamames, and M.J.Ramos (2011).
Metals in proteins: cluster analysis studies.
  J Mol Model, 17, 429-442.  
21439834 J.Tang, G.C.Lander, A.Olia, R.Li, S.Casjens, P.Prevelige, G.Cingolani, T.S.Baker, and J.E.Johnson (2011).
Peering down the barrel of a bacteriophage portal: the genome packaging and release valve in p22.
  Structure, 19, 496-502.  
19482036 A.Bhardwaj, N.Walker-Kopp, S.R.Casjens, and G.Cingolani (2009).
An evolutionarily conserved family of virion tail needles related to bacteriophage P22 gp26: correlation between structural stability and length of the alpha-helical trimeric coiled coil.
  J Mol Biol, 391, 227-245.  
19523897 G.C.Lander, R.Khayat, R.Li, P.E.Prevelige, C.S.Potter, B.Carragher, and J.E.Johnson (2009).
The P22 tail machine at subnanometer resolution reveals the architecture of an infection conduit.
  Structure, 17, 789-799.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.