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PDBsum entry 1hxs

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protein ligands Protein-protein interface(s) links
Virus PDB id
1hxs
Jmol
Contents
Protein chains
288 a.a. *
267 a.a. *
235 a.a. *
68 a.a. *
Ligands
MYR
PLM
Waters ×545
* Residue conservation analysis
PDB id:
1hxs
Name: Virus
Title: Crystal structure of mahoney strain of poliovirus at 2.2a re
Structure: Genome polyprotein, coat protein vp1. Chain: 1. Fragment: residues 579-880. Genome polyprotein, coat protein vp2. Chain: 2. Fragment: residues 69-340. Genome polyprotein, coat protein vp3. Chain: 3. Fragment: residues 341-577.
Source: Human poliovirus 1. Organism_taxid: 12081. Strain: mahoney. Strain: mahoney
Resolution:
2.20Å     R-factor:   0.268    
Authors: S.T.Miller,J.M.Hogle,D.J.Filman
Key ref:
S.T.Miller et al. (2001). Ab initio phasing of high-symmetry macromolecular complexes: successful phasing of authentic poliovirus data to 3.0 A resolution. J Mol Biol, 307, 499-512. PubMed id: 11254378 DOI: 10.1006/jmbi.2001.4485
Date:
16-Jan-01     Release date:   16-Jan-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03300  (POLG_POL1M) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2209 a.a.
288 a.a.*
Protein chain
Pfam   ArchSchema ?
P03300  (POLG_POL1M) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2209 a.a.
267 a.a.
Protein chain
Pfam   ArchSchema ?
P03300  (POLG_POL1M) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2209 a.a.
235 a.a.*
Protein chain
Pfam   ArchSchema ?
P03300  (POLG_POL1M) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2209 a.a.
68 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: Chains 1, 2, 3, 4: E.C.2.7.7.48  - RNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
   Enzyme class 3: Chains 1, 2, 3, 4: E.C.3.4.22.28  - Picornain 3C.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
   Enzyme class 4: Chains 1, 2, 3, 4: E.C.3.4.22.29  - Picornain 2A.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
   Enzyme class 5: Chains 1, 2, 3, 4: E.C.3.6.1.15  - Nucleoside-triphosphate phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NTP + H2O = NDP + phosphate
NTP
+ H(2)O
= NDP
+ phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     viral capsid   1 term 
  Biochemical function     structural molecule activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2001.4485 J Mol Biol 307:499-512 (2001)
PubMed id: 11254378  
 
 
Ab initio phasing of high-symmetry macromolecular complexes: successful phasing of authentic poliovirus data to 3.0 A resolution.
S.T.Miller, J.M.Hogle, D.J.Filman.
 
  ABSTRACT  
 
A genetic algorithm-based computational method for the ab initio phasing of diffraction data from crystals of symmetric macromolecular structures, such as icosahedral viruses, has been implemented and applied to authentic data from the P1/Mahoney strain of poliovirus. Using only single-wavelength native diffraction data, the method is shown to be able to generate correct phases, and thus electron density, to 3.0 A resolution. Beginning with no advance knowledge of the shape of the virus and only approximate knowledge of its size, the method uses a genetic algorithm to determine coarse, low-resolution (here, 20.5 A) models of the virus that obey the known non-crystallographic symmetry (NCS) constraints. The best scoring of these models are subjected to refinement and NCS-averaging, with subsequent phase extension to high resolution (3.0 A). Initial difficulties in phase extension were overcome by measuring and including all low-resolution terms in the transform. With the low-resolution data included, the method was successful in generating essentially correct phases and electron density to 6.0 A in every one of ten trials from different models identified by the genetic algorithm. Retrospective analysis revealed that these correct high-resolution solutions converged from a range of significantly different low-resolution phase sets (average differences of 59.7 degrees below 24 A). This method represents an efficient way to determine phases for icosahedral viruses, and has the advantage of producing phases free from model bias. It is expected that the method can be extended to other protein systems with high NCS.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The unique volume used to model the virus at low resolution is the four-sided pyramid enclosed by planes connecting one 5-fold, two 2-fold, and one 3-fold axis and extending safely beyond the estimated radius of the virus particle. In the model, this volume is sampled by a lattice of 99 point-scatterers. The indicated volume between 5-fold axes accommodates a regular tetrahedral lattice with a minimum of distortion.
Figure 3.
Figure 3. Plot of the electron density of the top-scoring solution from the GA after refinement and 20 cycles of NCS averaging. The density is non-continuous and there are extraneous peaks and minima. Nevertheless, the protein/solvent boundary is well defined and some large virus features are visible (most notably the mesa at the 5-fold axis). The structure as determined here is a Babinet solution, hence the density in the protein/RNA region is negative (broken line). Map borders correspond to the 320.50 Å and 377.10 Å unit cell edges.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 499-512) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19905490 X.Liu, and W.P.Su (2009).
Multiresolution phase extension of a trypsin inhibitor structure from 5 A to 2 A based on diffraction amplitudes alone.
  Phys Rev E Stat Nonlin Soft Matter Phys, 80, 047701.  
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.