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PDBsum entry 2ms2
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protein Protein-protein interface(s) links
Virus PDB id
2ms2

 

 

 

 

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Contents
Protein chains
129 a.a. *
Waters ×170
* Residue conservation analysis
PDB id:
2ms2
Name: Virus
Title: The refined structure of bacteriophage ms2 at 2.8 angstroms resolution
Structure: Bacteriophage ms2 coat protein. Chain: a, b, c. Engineered: yes
Source: Enterobacterio phage ms2. Organism_taxid: 12022
Resolution:
2.80Å     R-factor:   0.189    
Authors: K.Valegard,L.Liljas
Key ref: R.Golmohammadi et al. (1993). The refined structure of bacteriophage MS2 at 2.8 A resolution. J Mol Biol, 234, 620-639. PubMed id: 8254664
Date:
23-Aug-94     Release date:   26-Jan-95    
Supersedes: 1ms2
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P03612  (CAPSD_BPMS2) -  Capsid protein from Escherichia phage MS2
Seq:
Struc: 		130 a.a.
129 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
J Mol Biol 234:620-639 (1993)
PubMed id: 8254664  
 
 
The refined structure of bacteriophage MS2 at 2.8 A resolution.
R.Golmohammadi, K.Valegård, K.Fridborg, L.Liljas.
 
  ABSTRACT  
 
Bacteriophage MS2 is an icosahedral virus with 180 copies of a coat protein forming a shell around a single-stranded RNA molecule. The coat protein subunits form a lattice with the triangulation number T = 3. The coat protein has a fold which is different from the fold of all other viral coat proteins so far known. It consists of a five-stranded beta sheet facing the inside of the particle, and a hairpin and two helices on the outside. The crystal structure has been refined at 2.8 A resolution. The final R-factor was 0.189 for reflections with F > 2 sigma, and the root-mean-square deviation from idealized bond lengths and bond angles was 0.015 A and 2.9 degrees, respectively. The three chemically identical conformers A, B and C are largely similar. The B conformer has a unique conformation in one loop, which is involved in 5-fold interactions, while the A and C conformers, which are involved in the quasi-6-fold contacts, are similar throughout the structure. One cis-proline has been identified in the B conformer but the corresponding prolines in A and C are of the trans isomer. This residue is conserved within small RNA coliphages and it is proposed that this isomerization enables a less elongated loop (FG) around the 5-fold axis, thus creating a channel. The extensive dimer contact supports the idea of dimers as initial building blocks. An assembly pathway is proposed where five dimers converge into a pentamer and 12 pentamers are linked together with free dimers creating a complete particle.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21376055 K.Toropova, P.G.Stockley, and N.A.Ranson (2011).
Visualising a viral RNA genome poised for release from its receptor complex.
  J Mol Biol, 408, 408-419.  
20365771 E.C.Dykeman, and R.Twarock (2010).
All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein.
  Phys Rev E Stat Nonlin Soft Matter Phys, 81, 031908.  
21036656 K.J.Koudelka, and M.Manchester (2010).
Chemically modified viruses: principles and applications.
  Curr Opin Chem Biol, 14, 810-817.  
20872636 T.W.Knapman, V.L.Morton, N.J.Stonehouse, P.G.Stockley, and A.E.Ashcroft (2010).
Determining the topology of virus assembly intermediates using ion mobility spectrometry-mass spectrometry.
  Rapid Commun Mass Spectrom, 24, 3033-3042.  
20877857 V.L.Morton, W.Burkitt, G.O'Connor, N.J.Stonehouse, P.G.Stockley, and A.E.Ashcroft (2010).
RNA-induced conformational changes in a viral coat protein studied by hydrogen/deuterium exchange mass spectrometry.
  Phys Chem Chem Phys, 12, 13468-13475.  
19801477 E.Vo, S.Rengasamy, and R.Shaffer (2009).
Development of a test system to evaluate procedures for decontamination of respirators containing viral droplets.
  Appl Environ Microbiol, 75, 7303-7309.  
19289214 S.Katen, and A.Zlotnick (2009).
The thermodynamics of virus capsid assembly.
  Methods Enzymol, 455, 395-417.  
18979101 T.Keef, and R.Twarock (2009).
Affine extensions of the icosahedral group with applications to the three-dimensional organisation of simple viruses.
  J Math Biol, 59, 287-313.  
18460158 A.A.Akunyili, M.Alfatlawi, B.Upadhyaya, L.S.Rhoads, H.Eichelberger, and C.T.Van Bell (2008).
Ingestion without inactivation of bacteriophages by Tetrahymena.
  J Eukaryot Microbiol, 55, 207-213.  
18508079 D.S.Peabody, B.Manifold-Wheeler, A.Medford, S.K.Jordan, J.do Carmo Caldeira, and B.Chackerian (2008).
Immunogenic display of diverse peptides on virus-like particles of RNA phage MS2.
  J Mol Biol, 380, 252-263.  
18192368 J.Langlet, F.Gaboriaud, C.Gantzer, and J.F.Duval (2008).
Impact of chemical and structural anisotropy on the electrophoretic mobility of spherical soft multilayer particles: the case of bacteriophage MS2.
  Biophys J, 94, 3293-3312.  
18437498 J.M.Hooker, J.P.O'Neil, D.W.Romanini, S.E.Taylor, and M.B.Francis (2008).
Genome-free viral capsids as carriers for positron emission tomography radiolabels.
  Mol Imaging Biol, 10, 182-191.  
18662904 P.Plevka, K.Tars, and L.Liljas (2008).
Crystal packing of a bacteriophage MS2 coat protein mutant corresponds to octahedral particles.
  Protein Sci, 17, 1731-1739.
PDB code: 2vtu
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.  
18039380 J.C.Caldeira, and D.S.Peabody (2007).
Stability and assembly in vitro of bacteriophage PP7 virus-like particles.
  J Nanobiotechnology, 5, 10.  
17953574 J.Langlet, F.Gaboriaud, and C.Gantzer (2007).
Effects of pH on plaque forming unit counts and aggregation of MS2 bacteriophage.
  J Appl Microbiol, 103, 1632-1638.  
16408084 A.H.Andreotti (2006).
Opening the pore hinges on proline.
  Nat Chem Biol, 2, 13-14.  
17041164 J.Simonet, and C.Gantzer (2006).
Inactivation of poliovirus 1 and F-specific RNA phages and degradation of their genomes by UV irradiation at 254 nanometers.
  Appl Environ Microbiol, 72, 7671-7677.  
16531233 W.T.Horn, K.Tars, E.Grahn, C.Helgstrand, A.J.Baron, H.Lago, C.J.Adams, D.S.Peabody, S.E.Phillips, N.J.Stonehouse, L.Liljas, and P.G.Stockley (2006).
Structural basis of RNA binding discrimination between bacteriophages Qbeta and MS2.
  Structure, 14, 487-495.
PDB codes: 1zse 2b2d 2b2e 2b2g 2bny 2bq5 2bs0 2bs1
16313415 C.J.Hogan, E.M.Kettleson, M.H.Lee, B.Ramaswami, L.T.Angenent, and P.Biswas (2005).
Sampling methodologies and dosage assessment techniques for submicrometre and ultrafine virus aerosol particles.
  J Appl Microbiol, 99, 1422-1434.  
15687210 E.J.van Schaik, C.L.Giltner, G.F.Audette, D.W.Keizer, D.L.Bautista, C.M.Slupsky, B.D.Sykes, and R.T.Irvin (2005).
DNA binding: a novel function of Pseudomonas aeruginosa type IV pili.
  J Bacteriol, 187, 1455-1464.  
15071181 A.Fokine, P.R.Chipman, P.G.Leiman, V.V.Mesyanzhinov, V.B.Rao, and M.G.Rossmann (2004).
Molecular architecture of the prolate head of bacteriophage T4.
  Proc Natl Acad Sci U S A, 101, 6003-6008.  
14686926 S.M.Lima, D.S.Peabody, J.L.Silva, and A.C.de Oliveira (2004).
Mutations in the hydrophobic core and in the protein-RNA interface affect the packing and stability of icosahedral viruses.
  Eur J Biochem, 271, 135-145.  
15496523 W.T.Horn, M.A.Convery, N.J.Stonehouse, C.J.Adams, L.Liljas, S.E.Phillips, and P.G.Stockley (2004).
The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions.
  RNA, 10, 1776-1782.
PDB code: 1u1y
12770895 C.D.Anobom, S.C.Albuquerque, F.P.Albernaz, A.C.Oliveira, J.L.Silva, D.S.Peabody, A.P.Valente, and F.C.Almeida (2003).
Structural studies of MS2 bacteriophage virus particle disassembly by nuclear magnetic resonance relaxation measurements.
  Biophys J, 84, 3894-3903.  
  12890286 D.S.Peabody (2003).
A Viral Platform for Chemical Modification and Multivalent Display.
  J Nanobiotechnology, 1, 5.  
11713333 D.S.Peabody, and L.Al-Bitar (2001).
Isolation of viral coat protein mutants with altered assembly and aggregation properties.
  Nucleic Acids Res, 29, E113.  
  11720290 E.Grahn, T.Moss, C.Helgstrand, K.Fridborg, M.Sundaram, K.Tars, H.Lago, N.J.Stonehouse, D.R.Davis, P.G.Stockley, and L.Liljas (2001).
Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex.
  RNA, 7, 1616-1627.
PDB codes: 1e6t 1e7x 2bu1 2c4q 2c4y 2c4z 2c50 2c51
11170383 R.Tuma, H.Tsuruta, J.M.Benevides, P.E.Prevelige, and G.J.Thomas (2001).
Characterization of subunit structural changes accompanying assembly of the bacteriophage P22 procapsid.
  Biochemistry, 40, 665-674.  
11222721 Y.S.Nam, A.Petrovic, K.S.Jeong, and S.Venkatesan (2001).
Exchange of the basic domain of human immunodeficiency virus type 1 Rev for a polyarginine stretch expands the RNA binding specificity, and a minimal arginine cluster is required for optimal RRE RNA binding affinity, nuclear accumulation, and trans-activation.
  J Virol, 75, 2957-2971.  
11095669 E.Grahn, N.J.Stonehouse, C.J.Adams, K.Fridborg, L.Beigelman, J.Matulic-Adamic, S.L.Warriner, P.G.Stockley, and L.Liljas (2000).
Deletion of a single hydrogen bonding atom from the MS2 RNA operator leads to dramatic rearrangements at the RNA-coat protein interface.
  Nucleic Acids Res, 28, 4611-4616.
PDB codes: 1dzs 1h8j 1hdw 1he0 1he6 2iz9
10739912 K.Tars, K.Fridborg, M.Bundule, and L.Liljas (2000).
Structure determination of bacteriophage PP7 from Pseudomonas aeruginosa: from poor data to a good map.
  Acta Crystallogr D Biol Crystallogr, 56, 398-405.
PDB code: 1dwn
10464269 D.S.Peabody, and A.Chakerian (1999).
Asymmetric contributions to RNA binding by the Thr(45) residues of the MS2 coat protein dimer.
  J Biol Chem, 274, 25403-25410.  
9917072 E.Grahn, N.J.Stonehouse, J.B.Murray, S.van den Worm, K.Valegård, K.Fridborg, P.G.Stockley, and L.Liljas (1999).
Crystallographic studies of RNA hairpins in complexes with recombinant MS2 capsids: implications for binding requirements.
  RNA, 5, 131-138.
PDB codes: 1zdj 1zdk
9469846 H.Lago, S.A.Fonseca, J.B.Murray, N.J.Stonehouse, and P.G.Stockley (1998).
Dissecting the key recognition features of the MS2 bacteriophage translational repression complex.
  Nucleic Acids Res, 26, 1337-1344.  
9461079 M.A.Convery, S.Rowsell, N.J.Stonehouse, A.D.Ellington, I.Hirao, J.B.Murray, D.S.Peabody, S.E.Phillips, and P.G.Stockley (1998).
Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution.
  Nat Struct Biol, 5, 133-139.
PDB code: 6msf
9449365 M.S.Chapman (1998).
Watching one's P's and Q's: promiscuity, plasticity, and quasiequivalence in a T = 1 virus.
  Biophys J, 74, 639-644.  
10333745 R.N.De Guzman, R.B.Turner, and M.F.Summers (1998).
Protein-RNA recognition.
  Biopolymers, 48, 181-195.  
9469847 S.H.van den Worm, N.J.Stonehouse, K.Valegârd, J.B.Murray, C.Walton, K.Fridborg, P.G.Stockley, and L.Liljas (1998).
Crystal structures of MS2 coat protein mutants in complex with wild-type RNA operator fragments.
  Nucleic Acids Res, 26, 1345-1351.
PDB codes: 1aq3 1aq4 1mva 1mvb
9808042 S.Rowsell, N.J.Stonehouse, M.A.Convery, C.J.Adams, A.D.Ellington, I.Hirao, D.S.Peabody, P.G.Stockley, and S.E.Phillips (1998).
Crystal structures of a series of RNA aptamers complexed to the same protein target.
  Nat Struct Biol, 5, 970-975.
PDB codes: 5msf 7msf
9207028 M.Spingola, and D.S.Peabody (1997).
MS2 coat protein mutants which bind Qbeta RNA.
  Nucleic Acids Res, 25, 2808-2815.  
9092675 S.Wang, H.L.True, E.M.Seitz, K.A.Bennett, D.E.Fouts, J.F.Gardner, and D.W.Celander (1997).
Direct genetic selection of two classes of R17/MS2 coat proteins with altered capsid assembly properties and expanded RNA-binding activities.
  Nucleic Acids Res, 25, 1649-1657.  
  8976557 C.Z.Ni, C.A.White, R.S.Mitchell, J.Wickersham, R.Kodandapani, D.S.Peabody, and K.R.Ely (1996).
Crystal structure of the coat protein from the GA bacteriophage: model of the unassembled dimer.
  Protein Sci, 5, 2485-2493.
PDB code: 1una
8710507 D.S.Peabody, and F.Lim (1996).
Complementation of RNA binding site mutations in MS2 coat protein heterodimers.
  Nucleic Acids Res, 24, 2352-2359.  
  9003760 K.A.LeCuyer, L.S.Behlen, and O.C.Uhlenbeck (1996).
Mutagenesis of a stacking contact in the MS2 coat protein-RNA complex.
  EMBO J, 15, 6847-6853.  
8696973 K.Nagai (1996).
RNA-protein complexes.
  Curr Opin Struct Biol, 6, 53-61.  
8736553 R.Golmohammadi, K.Fridborg, M.Bundule, K.Valegård, and L.Liljas (1996).
The crystal structure of bacteriophage Q beta at 3.5 A resolution.
  Structure, 4, 543-554.
PDB code: 1qbe
7788292 C.Z.Ni, R.Syed, R.Kodandapani, J.Wickersham, D.S.Peabody, and K.R.Ely (1995).
Crystal structure of the MS2 coat protein dimer: implications for RNA binding and virus assembly.
  Structure, 3, 255-263.
PDB code: 1msc
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 code is shown on the right.

 

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