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BMRB: 5275

1KQR

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)

	Total	¹H	¹³C	¹⁵N
All	79.6 % (1697 of 2133)	82.3 % (901 of 1095)	74.7 % (626 of 838)	85.0 % (170 of 200)
Backbone	89.2 % (969 of 1086)	89.1 % (328 of 368)	89.2 % (488 of 547)	89.5 % (153 of 171)
Sidechain	72.3 % (884 of 1222)	78.8 % (573 of 727)	63.1 % (294 of 466)	58.6 % (17 of 29)
Aromatic	51.0 % (105 of 206)	91.3 % (94 of 103)	8.1 % (8 of 99)	75.0 % (3 of 4)
Methyl	87.1 % (176 of 202)	89.1 % (90 of 101)	85.1 % (86 of 101)

1. rotavirus VP4

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Concentration
1	rotavirus VP4	[U-15N]	1 mM
2	NaPO4		20 mM
3	NaCl		10 mM
4	Na azide		0.02 %
5	D2O		10 %
6	H2O		90 %

Sample #2

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

#	Name	Isotope labeling	Concentration
7	rotavirus VP4	[U-15N; U-13C; U-2H]	1 mM
8	NaPO4		20 mM
9	NaCl		10 mM
10	Na azide		0.02 %
11	D2O		10 %
12	H2O		90 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.18 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.18 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: -0.17 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

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 , Abstract

Show more 5 citaions

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 , Abstract

Citation 3

The program XEASY for computer-supported NMR spectral analysis of biological macromolecules
J. Biomol. NMR (1995), 6, 1-10, PubMed 22911575 , DOI 10.1007/BF00417486 , Abstract

Citation 4

Torsion angle dynamics for NMR structure calculation with the new program DYANA
Guntert, P., Mumenthaler, C., Wuthrich, K.
J. Mol. Biol. (1997), 273, 283-298, PubMed 9367762 , DOI 10.1006/jmbi.1997.1284 , Abstract

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 , Abstract

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 , Abstract

Hide non-primary 5 citaions

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    Title VP4_ROTRH Entity Outer capsid protein VP4

Related entities 1. sialic acid binding domain of rhesus rotavirus VP4, : 1 : 5 : 1 : 4 : 103 entities Detail

Experiments performed 17 experiments Detail

#	Name	Isotope labeling	Concentration
13	rotavirus VP4	[U-15N]-Ile	0.1 mM
14	NaPO4		20 mM
15	NaCl		10 mM
16	Na azide		0.02 %
17	D2O		10 %
18	H2O		90 %

#	Name	Isotope labeling	Concentration
19	rotavirus VP4	[U-15N]-Leu	0.1 mM
20	NaPO4		20 mM
21	NaCl		10 mM
22	Na azide		0.02 %
23	D2O		10 %
24	H2O		90 %

#	Name	Isotope labeling	Concentration
25	rotavirus VP4	[U-15N]-Phe	0.1 mM
26	NaPO4		20 mM
27	NaCl		10 mM
28	Na azide		0.02 %
29	D2O		10 %
30	H2O		90 %

#	Name	Isotope labeling	Concentration
31	rotavirus VP4	[U-15N]-Tyr	0.1 mM
32	NaPO4		20 mM
33	NaCl		10 mM
34	Na azide		0.02 %
35	D2O		10 %
36	H2O		90 %

#	Name	Isotope labeling	Concentration
37	rotavirus VP4	[U-15N]-Val	0.1 mM
38	NaPO4		20 mM
39	NaCl		10 mM
40	Na azide		0.02 %
41	D2O		10 %

#	Name	Isotope labeling	Concentration
42	rotavirus VP4	[U-15N; U-13C]	1 mM
43	NaPO4		20 mM
44	NaCl		10 mM
45	Na azide		0.02 %
46	D2O		10 %
47	H2O		90 %

#	Name	Isotope labeling	Concentration
48	rotavirus VP4	[U-13C]	1 mM
49	NaPO4		20 mM
50	NaCl		10 mM
51	Na azide		0.02 %
52	D2O		100 %

#	Name	Isotope labeling	Concentration
13	rotavirus VP4	[U-15N]-Ile	0.1 mM
14	NaPO4		20 mM
15	NaCl		10 mM
16	Na azide		0.02 %
17	D2O		10 %
18	H2O		90 %

#	Name	Isotope labeling	Concentration
19	rotavirus VP4	[U-15N]-Leu	0.1 mM
20	NaPO4		20 mM
21	NaCl		10 mM
22	Na azide		0.02 %
23	D2O		10 %
24	H2O		90 %

#	Name	Isotope labeling	Concentration
25	rotavirus VP4	[U-15N]-Phe	0.1 mM
26	NaPO4		20 mM
27	NaCl		10 mM
28	Na azide		0.02 %
29	D2O		10 %
30	H2O		90 %

#	Name	Isotope labeling	Concentration
31	rotavirus VP4	[U-15N]-Tyr	0.1 mM
32	NaPO4		20 mM
33	NaCl		10 mM
34	Na azide		0.02 %
35	D2O		10 %
36	H2O		90 %

#	Name	Isotope labeling	Concentration
37	rotavirus VP4	[U-15N]-Val	0.1 mM
38	NaPO4		20 mM
39	NaCl		10 mM
40	Na azide		0.02 %
41	D2O		10 %

#	Name	Isotope labeling	Concentration
42	rotavirus VP4	[U-15N; U-13C]	1 mM
43	NaPO4		20 mM
44	NaCl		10 mM
45	Na azide		0.02 %
46	D2O		10 %
47	H2O		90 %

#	Name	Isotope labeling	Concentration
48	rotavirus VP4	[U-13C]	1 mM
49	NaPO4		20 mM
50	NaCl		10 mM
51	Na azide		0.02 %
52	D2O		100 %

#	Name	Isotope labeling	Concentration
13	rotavirus VP4	[U-15N]-Ile	0.1 mM
14	NaPO4		20 mM
15	NaCl		10 mM
16	Na azide		0.02 %
17	D2O		10 %
18	H2O		90 %

#	Name	Isotope labeling	Concentration
19	rotavirus VP4	[U-15N]-Leu	0.1 mM
20	NaPO4		20 mM
21	NaCl		10 mM
22	Na azide		0.02 %
23	D2O		10 %
24	H2O		90 %

#	Name	Isotope labeling	Concentration
25	rotavirus VP4	[U-15N]-Phe	0.1 mM
26	NaPO4		20 mM
27	NaCl		10 mM
28	Na azide		0.02 %
29	D2O		10 %
30	H2O		90 %

#	Name	Isotope labeling	Concentration
31	rotavirus VP4	[U-15N]-Tyr	0.1 mM
32	NaPO4		20 mM
33	NaCl		10 mM
34	Na azide		0.02 %
35	D2O		10 %
36	H2O		90 %

#	Name	Isotope labeling	Concentration
37	rotavirus VP4	[U-15N]-Val	0.1 mM
38	NaPO4		20 mM
39	NaCl		10 mM
40	Na azide		0.02 %
41	D2O		10 %

#	Name	Isotope labeling	Concentration
42	rotavirus VP4	[U-15N; U-13C]	1 mM
43	NaPO4		20 mM
44	NaCl		10 mM
45	Na azide		0.02 %
46	D2O		10 %
47	H2O		90 %

#	Name	Isotope labeling	Concentration
48	rotavirus VP4	[U-13C]	1 mM
49	NaPO4		20 mM
50	NaCl		10 mM
51	Na azide		0.02 %
52	D2O		100 %

#	Name	Isotope labeling	Concentration
13	rotavirus VP4	[U-15N]-Ile	0.1 mM
14	NaPO4		20 mM
15	NaCl		10 mM
16	Na azide		0.02 %
17	D2O		10 %
18	H2O		90 %

#	Name	Isotope labeling	Concentration
19	rotavirus VP4	[U-15N]-Leu	0.1 mM
20	NaPO4		20 mM
21	NaCl		10 mM
22	Na azide		0.02 %
23	D2O		10 %
24	H2O		90 %

#	Name	Isotope labeling	Concentration
25	rotavirus VP4	[U-15N]-Phe	0.1 mM
26	NaPO4		20 mM
27	NaCl		10 mM
28	Na azide		0.02 %
29	D2O		10 %
30	H2O		90 %

#	Name	Isotope labeling	Concentration
31	rotavirus VP4	[U-15N]-Tyr	0.1 mM
32	NaPO4		20 mM
33	NaCl		10 mM
34	Na azide		0.02 %
35	D2O		10 %
36	H2O		90 %

#	Name	Isotope labeling	Concentration
37	rotavirus VP4	[U-15N]-Val	0.1 mM
38	NaPO4		20 mM
39	NaCl		10 mM
40	Na azide		0.02 %
41	D2O		10 %

#	Name	Isotope labeling	Concentration
42	rotavirus VP4	[U-15N; U-13C]	1 mM
43	NaPO4		20 mM
44	NaCl		10 mM
45	Na azide		0.02 %
46	D2O		10 %
47	H2O		90 %

#	Name	Isotope labeling	Concentration
48	rotavirus VP4	[U-13C]	1 mM
49	NaPO4		20 mM
50	NaCl		10 mM
51	Na azide		0.02 %
52	D2O		100 %

#	Name	Isotope labeling	Concentration
13	rotavirus VP4	[U-15N]-Ile	0.1 mM
14	NaPO4		20 mM
15	NaCl		10 mM
16	Na azide		0.02 %
17	D2O		10 %
18	H2O		90 %

#	Name	Isotope labeling	Concentration
19	rotavirus VP4	[U-15N]-Leu	0.1 mM
20	NaPO4		20 mM
21	NaCl		10 mM
22	Na azide		0.02 %
23	D2O		10 %
24	H2O		90 %

#	Name	Isotope labeling	Concentration
25	rotavirus VP4	[U-15N]-Phe	0.1 mM
26	NaPO4		20 mM
27	NaCl		10 mM
28	Na azide		0.02 %
29	D2O		10 %
30	H2O		90 %

#	Name	Isotope labeling	Concentration
31	rotavirus VP4	[U-15N]-Tyr	0.1 mM
32	NaPO4		20 mM
33	NaCl		10 mM
34	Na azide		0.02 %
35	D2O		10 %
36	H2O		90 %

#	Name	Isotope labeling	Concentration
37	rotavirus VP4	[U-15N]-Val	0.1 mM
38	NaPO4		20 mM
39	NaCl		10 mM
40	Na azide		0.02 %
41	D2O		10 %

nullKeywords rotavirus, VP4, VP8*, spike protein, outer capsid, sialic acid, hemagglutinin, cell attachment, neutralization antigen, lectin, galectin fold

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Found 1 Document (5.303 seconds)

BMRB: 5275

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 59, Swiss-Prot: 1 entries Detail

Related entities 1. sialic acid binding domain of rhesus rotavirus VP4, : 1 : 5 : 1 : 4 : 103 entities Detail

Experiments performed 17 experiments Detail

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