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PDBsum entry 1js9
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protein ligands metals Protein-protein interface(s) links
Virus PDB id
1js9

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
149 a.a.
165 a.a.
189 a.a.
Ligands
P6G
Metals
_MG ×2
PDB id:
1js9
Name: Virus
Title: Brome mosaic virus
Structure: Coat protein. Chain: a, b, c. Synonym: capsid protein
Source: Brome mosaic virus. Organism_taxid: 12302. Strain: dickson
Resolution:
3.40Å     R-factor:   0.238     R-free:   0.250
Authors: R.W.Lucas,S.B.Larson,A.Mcpherson
Key ref:
R.W.Lucas et al. (2002). The crystallographic structure of brome mosaic virus. J Mol Biol, 317, 95. PubMed id: 11916381 DOI: 10.1006/jmbi.2001.5389
Date:
16-Aug-01     Release date:   03-Apr-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P03602  (CAPSD_BMV) -  Capsid protein from Brome mosaic virus
Seq:
Struc: 		189 a.a.
149 a.a.
Protein chain
P03602  (CAPSD_BMV) -  Capsid protein from Brome mosaic virus
Seq:
Struc: 		189 a.a.
165 a.a.
Protein chain
P03602  (CAPSD_BMV) -  Capsid protein from Brome mosaic virus
Seq:
Struc: 		189 a.a.
189 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1006/jmbi.2001.5389 J Mol Biol 317:95 (2002)
PubMed id: 11916381  
 
 
The crystallographic structure of brome mosaic virus.
R.W.Lucas, S.B.Larson, A.McPherson.
 
  ABSTRACT  
 
The structure of brome mosaic virus (BMV), the type member of the bromoviridae family, has been determined from a single rhombohedral crystal by X-ray diffraction, and refined to an R value of 0.237 for data in the range 3.4-40.0 A. The structure, which represents the native, compact form at pH 5.2 in the presence of 0.1 M Mg(2+), was solved by molecular replacement using the model of cowpea chlorotic mottle virus (CCMV), which BMV closely resembles. The BMV model contains amino acid residues 41-189 for the pentameric capsid A subunits, and residues 25-189 and 1-189 for the B and C subunits, respectively, which compose the hexameric capsomeres. In the model there are two Mg ions and one molecule of polyethylene glycol (PEG). The first 25 amino acid residues of the C subunit are modeled as polyalanine. The coat protein has the canonical "jellyroll" beta-barrel topology with extended amino-terminal polypeptides as seen in other icosahedral plant viruses. Mass spectrometry shows that in native BMV virions, a significant fraction of the amino-terminal peptides are apparently cleaved. No recognizable nucleic acid residue is visible in the electron density maps except at low resolution where it appears to exhibit a layered arrangement in the virion interior. It is juxtaposed closely with the interior surface of the capsid but does not interpenetrate. The protein subunits forming hexameric capsomeres, and particularly dimers, appear to interact extensively, but the subunits otherwise contact one another sparsely about the 5-fold and quasi 3-fold axes. Thus, the virion appears to be an assembly of loosely associated hexameric capsomeres, which may be the basis for the swelling and dissociation that occurs at neutral pH and elevated salt concentration. A Mg ion is observed to lie exactly on the quasi-3-fold axis and is closely coordinated by side-chains of three quasi-symmetry-related residues glutamates 84, with possible participation of side-chains from threonines 145, and asparagines 148. A presumptive Mg(2+) is also present on the 5-fold axis where there is a concentration of negatively charged side-chains, but the precise coordination is unclear. In both cases these cations appear to be essential for maintenance of virion stability. Density that is contiguous with the viral interior is present on the 3-fold axis at the center of the hexameric capsomere, where there is a pore of about 6 A diameter. The density cannot be attributed to cations and it was modeled as a PEG molecule.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. The coordination of the Mg ion on the quasi-3-fold axis. The glutamate, threonine, and aspartate residues involved are labeled. These cations may serve a crucial role in the formation and maintenance of the capsid structure, and the carboxyl groups are likely those earlier identified as Caspar carboxyls.[13] 		Figure 8.
Figure 8. Backbone representation superimposing the BMV ABC trimer on the corresponding CCMV trimer, which is presented as a transparent overlay.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 317, 95-0) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21453435 C.C.Kao, P.Ni, M.Hema, X.Huang, and B.Dragnea (2011).
The coat protein leads the way: an update on basic and applied studies with the Brome mosaic virus coat protein.
  Mol Plant Pathol, 12, 403-412.  
21149971 O.M.Elrad, and M.F.Hagan (2010).
Encapsulation of a polymer by an icosahedral virus.
  Phys Biol, 7, 045003.  
19481091 G.Yi, R.C.Vaughan, I.Yarbrough, S.Dharmaiah, and C.C.Kao (2009).
RNA binding by the brome mosaic virus capsid protein and the regulation of viral RNA accumulation.
  J Mol Biol, 391, 314-326.  
19317561 M.F.Hagan (2009).
A theory for viral capsid assembly around electrostatic cores.
  J Chem Phys, 130, 114902.  
19572822 S.Franzen, and S.A.Lommel (2009).
Targeting cancer with 'smart bombs': equipping plant virus nanoparticles for a 'seek and destroy' mission.
  Nanomedicine (Lond), 4, 575-588.  
18754598 C.Chen, C.C.Kao, and B.Dragnea (2008).
Self-assembly of brome mosaic virus capsids: insights from shorter time-scale experiments.
  J Phys Chem A, 112, 9405-9412.  
18384150 K.S.Aragão, M.Satre, A.Imberty, and A.Varrot (2008).
Structure determination of Discoidin II from Dictyostelium discoideum and carbohydrate binding properties of the lectin domain.
  Proteins, 73, 43-52.
PDB codes: 2vm9 2vmc 2vmd 2vme
18643099 M.F.Hagan (2008).
Controlling viral capsid assembly with templating.
  Phys Rev E Stat Nonlin Soft Matter Phys, 77, 051904.  
18032497 P.Annamalai, F.Rofail, D.A.Demason, and A.L.Rao (2008).
Replication-coupled packaging mechanism in positive-strand RNA viruses: synchronized coexpression of functional multigenome RNA components of an animal and a plant virus in Nicotiana benthamiana cells by agroinfiltration.
  J Virol, 82, 1484-1495.  
  19809586 S.E.Aniagyei, C.Dufort, C.C.Kao, and B.Dragnea (2008).
Self-assembly approaches to nanomaterial encapsulation in viral protein cages.
  J Mater Chem, 18, 3763-3774.  
18066637 S.L.Calhoun, and A.L.Rao (2008).
Functional analysis of brome mosaic virus coat protein RNA-interacting domains.
  Arch Virol, 153, 231-245.  
18498137 V.L.Morton, P.G.Stockley, N.J.Stonehouse, and A.E.Ashcroft (2008).
Insights into virus capsid assembly from non-covalent mass spectrometry.
  Mass Spectrom Rev, 27, 575-595.  
17894371 J.E.Stone, J.C.Phillips, P.L.Freddolino, D.J.Hardy, L.G.Trabuco, and K.Schulten (2007).
Accelerating molecular modeling applications with graphics processors.
  J Comput Chem, 28, 2618-2640.  
17252611 J.N.Leonard, P.Ferstl, A.Delgado, and D.V.Schaffer (2007).
Enhanced preparation of adeno-associated viral vectors by using high hydrostatic pressure to selectively inactivate helper adenovirus.
  Biotechnol Bioeng, 97, 1170-1179.  
17227841 J.Sun, C.DuFort, M.C.Daniel, A.Murali, C.Chen, K.Gopinath, B.Stein, M.De, V.M.Rotello, A.Holzenburg, C.C.Kao, and B.Dragnea (2007).
Core-controlled polymorphism in virus-like particles.
  Proc Natl Acad Sci U S A, 104, 1354-1359.  
17728853 N.F.Steinmetz, and D.J.Evans (2007).
Utilisation of plant viruses in bionanotechnology.
  Org Biomol Chem, 5, 2891-2902.  
17005656 P.Annamalai, and A.L.Rao (2007).
In vivo packaging of brome mosaic virus RNA3, but not RNAs 1 and 2, is dependent on a cis-acting 3' tRNA-like structure.
  J Virol, 81, 173-181.  
17005687 P.Annamalai, and A.L.Rao (2006).
Packaging of brome mosaic virus subgenomic RNA is functionally coupled to replication-dependent transcription and translation of coat protein.
  J Virol, 80, 10096-10108.  
17090672 V.A.Belyi, and M.Muthukumar (2006).
Electrostatic origin of the genome packing in viruses.
  Proc Natl Acad Sci U S A, 103, 17174-17178.  
15731222 P.Annamalai, S.Apte, S.Wilkens, and A.L.Rao (2005).
Deletion of highly conserved arginine-rich RNA binding motif in cowpea chlorotic mottle virus capsid protein results in virion structural alterations and RNA packaging constraints.
  J Virol, 79, 3277-3288.  
15454465 M.Casselyn, A.Tardieu, H.Delacroix, and S.Finet (2004).
Birth and growth kinetics of brome mosaic virus microcrystals.
  Biophys J, 87, 2737-2748.  
14624862 A.Zlotnick, and S.J.Stray (2003).
How does your virus grow? Understanding and interfering with virus assembly.
  Trends Biotechnol, 21, 536-542.  
12941908 T.A.Damayanti, S.Tsukaguchi, K.Mise, and T.Okuno (2003).
cis-acting elements required for efficient packaging of brome mosaic virus RNA3 in barley protoplasts.
  J Virol, 77, 9979-9986.  
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.

 

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