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The rhesus rotavirus sialic acid binding domain without ligand
Authors
Wagner, G., Dormitzer, P.R., Sun, Z.J., Harrison, S.C.
Assembly
sialic acid binding domain of rhesus rotavirus VP4
Entity
1. sialic acid binding domain of rhesus rotavirus VP4 (polymer, Thiol state: all free), 186 monomers, 20805.77 Da Detail

APVNWGPGET NDSTTVEPVL DGPYQPTTFN PPVDYWMLLA PTAAGVVVEG TNNTDRWLAT ILVEPNVTSE TRSYTLFGTQ EQITIANASQ TQWKFIDVVK TTQNGSYSQY GPLQSTPKLY AVMKHNGKIY TYNGETPNVT TKYYSTTNYD SVNMTAFCDF YIIPREEEST CTEYINNGLP PIQNTR


Formula weight
20805.77 Da
Source organism
Simian rotavirus A strain RRV
Exptl. method
NMR
Refine. method
simulated annealing
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 90.3 %, Completeness: 79.6 %, Completeness (bb): 89.2 % Detail

Polymer type: polypeptide(L)

Total1H13C15N
All79.6 % (1697 of 2133)82.3 % (901 of 1095)74.7 % (626 of 838)85.0 % (170 of 200)
Backbone89.2 % (969 of 1086)89.1 % (328 of 368)89.2 % (488 of 547)89.5 % (153 of 171)
Sidechain72.3 % (884 of 1222)78.8 % (573 of 727)63.1 % (294 of 466)58.6 % (17 of 29)
Aromatic51.0 % (105 of 206)91.3 % (94 of 103) 8.1 % (8 of 99)75.0 % (3 of 4)
Methyl87.1 % (176 of 202)89.1 % (90 of 101)85.1 % (86 of 101)

1. rotavirus VP4

APVNWGPGET NDSTTVEPVL DGPYQPTTFN PPVDYWMLLA PTAAGVVVEG TNNTDRWLAT ILVEPNVTSE TRSYTLFGTQ EQITIANASQ TQWKFIDVVK TTQNGSYSQY GPLQSTPKLY AVMKHNGKIY TYNGETPNVT TKYYSTTNYD SVNMTAFCDF YIIPREEEST CTEYINNGLP PIQNTR

Sample #1

Pressure 1 atm, Temperature 298 (±1) K, pH 7.0 (±0.2)


#NameIsotope labelingTypeConcentration
1rotavirus VP4[U-15N]1 mM
2NaPO420 mM
3NaCl10 mM
4Na azide0.02 %
5D2O10 %
6H2O90 %
Sample #2

Pressure 1 atm, Temperature 298 (±1) K, pH 7.0 (±0.2)


#NameIsotope labelingTypeConcentration
7rotavirus VP4[U-15N; U-13C; U-2H]1 mM
8NaPO420 mM
9NaCl10 mM
10Na azide0.02 %
11D2O10 %
12H2O90 %

LACS Plot; CA
Referencing offset: 0.18 ppm, Outliers: 1 Detail
LACS Plot; CB
Referencing offset: 0.18 ppm, Outliers: 1 Detail
LACS Plot; HA
Referencing offset: -0.17 ppm, Outliers: 1 Detail
LACS Plot; CO
Referencing offset: 0.66 ppm, Outliers: 5 Detail
Protein Blocks Logo
Calculated from 20 models in PDB: 1KRI, Strand ID: A Detail


Release date
2002-03-21
Citation 1
The rhesus rotavirus VP4 sialic acid binding domain has a galectin fold with a novel carbohydrate binding site
Dormitzer, P.R., Sun, Z.J., Wagner, G., Harrison, S.C.
EMBO J. (2002), 21, 885-897, PubMed 11867517 , DOI 10.1093/emboj/21.5.885 ,
Citation 2
Proteolysis of monomeric recombinant rotavirus VP4 yields an oligomeric VP5* core
Dormitzer, P.R., Greenberg, H.B., Harrison, S.C.
J. Virol. (2001), 75, 7339-7350, PubMed 11462006 , DOI 10.1128/JVI.75.16.7339-7350.2001 ,
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Citation 5
Protein backbone angle restraints from searching a database for chemical shift and sequence homology
Cornilescu, G., Delaglio, F., Bax, A.
J. Biomol. NMR (1999), 13, 289-302, PubMed 10212987 ,
Citation 6
Crystallography & NMR system: A new software suite for macromolecular structure determination
Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.
Acta Crystallogr. D. Biol. Crystallogr. (1998), 54, 905-921, PubMed 9757107 , DOI: ,
Related entities 1. sialic acid binding domain of rhesus rotavirus VP4, : 1 : 5 : 1 : 4 : 103 entities Detail
Experiments performed 17 experiments Detail
nullKeywords rotavirus, VP4, VP8*, spike protein, outer capsid, sialic acid, hemagglutinin, cell attachment, neutralization antigen, lectin, galectin fold