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PDBsum entry 2obt
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Viral protein PDB id
2obt

 

 

 

 

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Contents
Protein chain
307 a.a. *
Ligands
GAL-FUC-GLA
Waters ×236
* Residue conservation analysis
PDB id:
2obt
Name: Viral protein
Title: Crystal structures of p domain of norovirus va387 in complex with blood group trisaccharides type b
Structure: Capsid protein. Chain: a. Fragment: p domain. Engineered: yes. Mutation: yes
Source: Norovirus. Organism_taxid: 142786. Strain: va387. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.00Å     R-factor:   0.214     R-free:   0.257
Authors: S.Cao,X.Li,Z.Rao
Key ref: S.Cao et al. (2007). Structural basis for the recognition of blood group trisaccharides by norovirus. J Virol, 81, 5949-5957. PubMed id: 17392366
Date:
20-Dec-06     Release date:   24-Apr-07    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q913Z3  (Q913Z3_9CALI) -  Capsid from Human calicivirus NLV/VA98387/1998
Seq:
Struc: 		 
Seq:
Struc: 		539 a.a.
307 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
J Virol 81:5949-5957 (2007)
PubMed id: 17392366  
 
 
Structural basis for the recognition of blood group trisaccharides by norovirus.
S.Cao, Z.Lou, M.Tan, Y.Chen, Y.Liu, Z.Zhang, X.C.Zhang, X.Jiang, X.Li, Z.Rao.
 
  ABSTRACT  
 
Noroviruses are one of the major causes of nonbacterial gastroenteritis epidemics in humans. Recent studies on norovirus receptors show that different noroviruses recognize different human histo-blood group antigens (HBGAs), and eight receptor binding patterns of noroviruses have been identified. The P domain of the norovirus capsids is directly involved in this recognition. To determine the precise locations and receptor binding modes of HBGA carbohydrates on the viral capsids, a recombinant P protein of a GII-4 strain norovirus, VA387, was cocrystallized with synthetic type A or B trisaccharides. Based on complex crystal structures observed at a 2.0-A resolution, we demonstrated that the receptor binding site lies at the outermost end of the P domain and forms an extensive hydrogen-bonding network with the saccharide ligand. The A and B trisaccharides display similar binding modes, and the common fucose ring plays a key role in this interaction. The extensive interface between the two protomers in a P dimer also plays a crucial role in the formation of the receptor binding interface.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21173246 K.Bok, G.I.Parra, T.Mitra, E.Abente, C.K.Shaver, D.Boon, R.Engle, C.Yu, A.Z.Kapikian, S.V.Sosnovtsev, R.H.Purcell, and K.Y.Green (2011).
Chimpanzees as an animal model for human norovirus infection and vaccine development.
  Proc Natl Acad Sci U S A, 108, 325-330.  
21310617 R.A.Bull, and P.A.White (2011).
Mechanisms of GII.4 norovirus evolution.
  Trends Microbiol, 19, 233-240.  
20504857 A.Porollo, and J.Meller (2010).
POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations.
  Nucleic Acids Res, 38, W662-W666.  
20407802 C.A.Koppisetty, W.Nasir, F.Strino, G.E.Rydell, G.Larson, and P.G.Nyholm (2010).
Computational studies on the interaction of ABO-active saccharides with the norovirus VA387 capsid protein can explain experimental binding data.
  J Comput Aided Mol Des, 24, 423-431.  
20125087 E.F.Donaldson, L.C.Lindesmith, A.D.Lobue, and R.S.Baric (2010).
Viral shape-shifting: norovirus evasion of the human immune system.
  Nat Rev Microbiol, 8, 231-241.  
20042616 G.Belliot, A.H.Kamel, M.Estienney, K.Ambert-Balay, and P.Pothier (2010).
Evidence of emergence of new GGII.4 norovirus variants from gastroenteritis outbreak survey in France during the 2007-to-2008 and 2008-to-2009 winter seasons.
  J Clin Microbiol, 48, 994-998.  
20848862 H.Sato (2010).
[Survival strategies of human norovirus].
  Uirusu, 60, 21-32.  
20463813 J.J.Siebenga, P.Lemey, S.L.Kosakovsky Pond, A.Rambaut, H.Vennema, and M.Koopmans (2010).
Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants.
  PLoS Pathog, 6, e1000884.  
20534859 K.Motomura, M.Yokoyama, H.Ode, H.Nakamura, H.Mori, T.Kanda, T.Oka, K.Katayama, M.Noda, T.Tanaka, N.Takeda, H.Sato, S.Yoshizumi, T.Mikami, H.Saito, Y.Ueki, A.Takahashi, T.Hebiguchi, K.Shinozaki, T.Yoshida, T.Tamura, T.Takizawa, M.Toho, S.Kobayashi, K.Uchino, N.Iritani, S.Iizuka, F.Itoh, S.Fukuda, R.Kondo, Y.Yamashita, S.Funatsumaru, Y.Matsuoka, and A.Iwakiri (2010).
Divergent evolution of norovirus GII/4 by genome recombination from May 2006 to February 2009 in Japan.
  J Virol, 84, 8085-8097.  
20218858 M.Herbst-Kralovetz, H.S.Mason, and Q.Chen (2010).
Norwalk virus-like particles as vaccines.
  Expert Rev Vaccines, 9, 299-307.  
20865168 M.Tan, and X.Jiang (2010).
Norovirus gastroenteritis, carbohydrate receptors, and animal models.
  PLoS Pathog, 6, 0.  
20709837 M.Zakhour, H.Maalouf, I.Di Bartolo, L.Haugarreau, F.S.Le Guyader, N.Ruvoën-Clouet, J.C.Le Saux, F.M.Ruggeri, M.Pommepuy, and J.Le Pendu (2010).
Bovine norovirus: carbohydrate ligand, environmental contamination, and potential cross-species transmission via oysters.
  Appl Environ Microbiol, 76, 6404-6411.  
20360972 R.A.Bull, J.S.Eden, W.D.Rawlinson, and P.A.White (2010).
Rapid evolution of pandemic noroviruses of the GII.4 lineage.
  PLoS Pathog, 6, e1000831.  
20335262 S.Taube, J.R.Rubin, U.Katpally, T.J.Smith, A.Kendall, J.A.Stuckey, and C.E.Wobus (2010).
High-resolution x-ray structure and functional analysis of the murine norovirus 1 capsid protein protruding domain.
  J Virol, 84, 5695-5705.
PDB codes: 3lq6 3lqe
20554772 T.Farkas, R.W.Cross, E.Hargitt, N.W.Lerche, A.L.Morrow, and K.Sestak (2010).
Genetic diversity and histo-blood group antigen interactions of rhesus enteric caliciviruses.
  J Virol, 84, 8617-8625.  
20592096 Y.Yang, M.Xia, M.Tan, P.Huang, W.Zhong, X.L.Pang, B.E.Lee, J.Meller, T.Wang, and X.Jiang (2010).
Genetic and phenotypic characterization of GII-4 noroviruses that circulated during 1987 to 2008.
  J Virol, 84, 9595-9607.  
19141453 B.Carlsson, A.M.Lindberg, J.Rodriguez-Díaz, K.O.Hedlund, B.Persson, and L.Svensson (2009).
Quasispecies dynamics and molecular evolution of human norovirus capsid P region during chronic infection.
  J Gen Virol, 90, 432-441.  
19440360 B.Carlsson, E.Kindberg, J.Buesa, G.E.Rydell, M.F.Lidón, R.Montava, R.A.Mallouh, A.Grahn, J.Rodríguez-Díaz, J.Bellido, A.Arnedo, G.Larson, and L.Svensson (2009).
The G428A Nonsense Mutation in FUT2 Provides Strong but Not Absolute Protection against Symptomatic GII.4 Norovirus Infection.
  PLoS ONE, 4, e5593.  
19426740 E.M.Grahn, H.C.Winter, H.Tateno, I.J.Goldstein, and U.Krengel (2009).
Structural characterization of a lectin from the mushroom Marasmius oreades in complex with the blood group B trisaccharide and calcium.
  J Mol Biol, 390, 457-466.
PDB code: 3ef2
19297483 J.L.Cannon, L.C.Lindesmith, E.F.Donaldson, L.Saxe, R.S.Baric, and J.Vinjé (2009).
Herd immunity to GII.4 noroviruses is supported by outbreak patient sera.
  J Virol, 83, 5363-5374.  
19759138 K.Bok, E.J.Abente, M.Realpe-Quintero, T.Mitra, S.V.Sosnovtsev, A.Z.Kapikian, and K.Y.Green (2009).
Evolutionary dynamics of GII.4 noroviruses over a 34-year period.
  J Virol, 83, 11890-11901.  
19285508 M.A.Higgins, D.W.Abbott, M.J.Boulanger, and A.B.Boraston (2009).
Blood group antigen recognition by a solute-binding protein from a serotype 3 strain of Streptococcus pneumoniae.
  J Mol Biol, 388, 299-309.
PDB code: 2w7y
19337380 M.Tan, M.Xia, Y.Chen, W.Bu, R.S.Hegde, J.Meller, X.Li, and X.Jiang (2009).
Conservation of carbohydrate binding interfaces: evidence of human HBGA selection in norovirus evolution.
  PLoS ONE, 4, e5058.  
19578439 M.Zakhour, N.Ruvoën-Clouet, A.Charpilienne, B.Langpap, D.Poncet, T.Peters, N.Bovin, and J.Le Pendu (2009).
The alphaGal epitope of the histo-blood group antigen family is a ligand for bovine norovirus Newbury2 expected to prevent cross-species transmission.
  PLoS Pathog, 5, e1000504.  
19622744 T.S.Guu, Z.Liu, Q.Ye, D.A.Mata, K.Li, C.Yin, J.Zhang, and Y.J.Tao (2009).
Structure of the hepatitis E virus-like particle suggests mechanisms for virus assembly and receptor binding.
  Proc Natl Acad Sci U S A, 106, 12992-12997.
PDB code: 3hag
19342221 T.Stehle, and J.M.Casasnovas (2009).
Specificity switching in virus-receptor complexes.
  Curr Opin Struct Biol, 19, 181-188.  
18809496 A.Imberty, and A.Varrot (2008).
Microbial recognition of human cell surface glycoconjugates.
  Curr Opin Struct Biol, 18, 567-576.  
18550656 D.Bhella, D.Gatherer, Y.Chaudhry, R.Pink, and I.G.Goodfellow (2008).
Structural insights into calicivirus attachment and uncoating.
  J Virol, 82, 8051-8058.  
18213393 D.J.Allen, J.J.Gray, C.I.Gallimore, J.Xerry, and M.Iturriza-Gómara (2008).
Analysis of Amino Acid Variation in the P2 Domain of the GII-4 Norovirus VP1 Protein Reveals Putative Variant-Specific Epitopes.
  PLoS ONE, 3, e1485.  
18701592 H.Shirato, S.Ogawa, H.Ito, T.Sato, A.Kameyama, H.Narimatsu, Z.Xiaofan, T.Miyamura, T.Wakita, K.Ishii, and N.Takeda (2008).
Noroviruses distinguish between type 1 and type 2 histo-blood group antigens for binding.
  J Virol, 82, 10756-10767.  
18599458 J.M.Choi, A.M.Hutson, M.K.Estes, and B.V.Prasad (2008).
Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus.
  Proc Natl Acad Sci U S A, 105, 9175-9180.
PDB codes: 2zl5 2zl6 2zl7
18292090 K.J.Gregg, R.Finn, D.W.Abbott, and A.B.Boraston (2008).
Divergent modes of glycan recognition by a new family of carbohydrate-binding modules.
  J Biol Chem, 283, 12604-12613.
PDB codes: 2vmg 2vmh 2vmi 2vng 2vno 2vnr
18768979 K.Motomura, T.Oka, M.Yokoyama, H.Nakamura, H.Mori, H.Ode, G.S.Hansman, K.Katayama, T.Kanda, T.Tanaka, N.Takeda, and H.Sato (2008).
Identification of monomorphic and divergent haplotypes in the 2006-2007 norovirus GII/4 epidemic population by genomewide tracing of evolutionary history.
  J Virol, 82, 11247-11262.  
18271619 L.C.Lindesmith, E.F.Donaldson, A.D.Lobue, J.L.Cannon, D.P.Zheng, J.Vinje, and R.S.Baric (2008).
Mechanisms of GII.4 norovirus persistence in human populations.
  PLoS Med, 5, e31.  
18725806 M.Koopmans (2008).
Progress in understanding norovirus epidemiology.
  Curr Opin Infect Dis, 21, 544-552.  
18480447 N.Iritani, H.Vennema, J.J.Siebenga, R.J.Siezen, B.Renckens, Y.Seto, A.Kaida, and M.Koopmans (2008).
Genetic analysis of the capsid gene of genotype GII.2 noroviruses.
  J Virol, 82, 7336-7345.  
18385236 W.Bu, A.Mamedova, M.Tan, M.Xia, X.Jiang, and R.S.Hegde (2008).
Structural basis for the receptor binding specificity of Norwalk virus.
  J Virol, 82, 5340-5347.
PDB codes: 3bqj 3by1 3by2 3by3 3d26
18838436 Y.Someya, N.Takeda, and T.Wakita (2008).
Saturation Mutagenesis reveals that GLU54 of Norovirus 3C-like Protease is not Essential for the Proteolytic Activity.
  J Biochem, 144, 771-780.  
18357756 H.Shirato-Horikoshi, and N.Takeda (2007).
[Interaction between noroviruses and human histo-blood group antigens]
  Uirusu, 57, 181-189.  
17609280 J.J.Siebenga, H.Vennema, B.Renckens, E.de Bruin, B.van der Veer, R.J.Siezen, and M.Koopmans (2007).
Epochal evolution of GGII.4 norovirus capsid proteins from 1995 to 2006.
  J Virol, 81, 9932-9941.  
17804495 V.P.Lochridge, and M.E.Hardy (2007).
A single-amino-acid substitution in the P2 domain of VP1 of murine norovirus is sufficient for escape from antibody neutralization.
  J Virol, 81, 12316-12322.  
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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