BMRB Entry 5275

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR5275
MolProbity Validation Chart

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Title:
The rhesus rotavirus sialic acid binding domain without ligand
Deposition date:
2002-02-06
Original release date:
2002-03-22
Authors:
Dormitzer, P.; Sun, Z.-Y.; Wagner, G.; Harrison, S.
Citation:

Citation: Dormitzer, P.; Sun, Z.-Y.; Wagner, G.; Harrison, S.. "The rhesus rotavirus VP4 sialic acid binding domain has a galectin fold with a novel carbohydrate binding site"  EMBO J. 21, 885-897 (2002).
PubMed: 11867517

Assembly members:

Assembly members:
rotavirus VP4, polymer, 186 residues, 20876 Da.

Natural source:

Natural source:   Common Name: rhesus rotavirus   Taxonomy ID: 10969   Superkingdom: Viruses   Kingdom: not available   Genus/species: Rhesus rotavirus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX-VP8(46-231)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
rotavirus VP4: APVNWGPGETNDSTTVEPVL DGPYQPTTFNPPVDYWMLLA PTAAGVVVEGTNNTDRWLAT ILVEPNVTSETRSYTLFGTQ EQITIANASQTQWKFIDVVK TTQNGSYSQYGPLQSTPKLY AVMKHNGKIYTYNGETPNVT TKYYSTTNYDSVNMTAFCDF YIIPREEESTCTEYINNGLP PIQNTR

Data sets:
Data typeCount
1H chemical shifts1030
13C chemical shifts573
15N chemical shifts168

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1sialic acid binding domain of rhesus rotavirus VP41

Entities:

Entity 1, sialic acid binding domain of rhesus rotavirus VP4 186 residues - 20876 Da.

1   ALAPROVALASNTRPGLYPROGLYGLUTHR
2   ASNASPSERTHRTHRVALGLUPROVALLEU
3   ASPGLYPROTYRGLNPROTHRTHRPHEASN
4   PROPROVALASPTYRTRPMETLEULEUALA
5   PROTHRALAALAGLYVALVALVALGLUGLY
6   THRASNASNTHRASPARGTRPLEUALATHR
7   ILELEUVALGLUPROASNVALTHRSERGLU
8   THRARGSERTYRTHRLEUPHEGLYTHRGLN
9   GLUGLNILETHRILEALAASNALASERGLN
10   THRGLNTRPLYSPHEILEASPVALVALLYS
11   THRTHRGLNASNGLYSERTYRSERGLNTYR
12   GLYPROLEUGLNSERTHRPROLYSLEUTYR
13   ALAVALMETLYSHISASNGLYLYSILETYR
14   THRTYRASNGLYGLUTHRPROASNVALTHR
15   THRLYSTYRTYRSERTHRTHRASNTYRASP
16   SERVALASNMETTHRALAPHECYSASPPHE
17   TYRILEILEPROARGGLUGLUGLUSERTHR
18   CYSTHRGLUTYRILEASNASNGLYLEUPRO
19   PROILEGLNASNTHRARG

Samples:

sample_1: rotavirus VP4, [U-15N], 1 mM; NaPO4 20 mM; NaCl 10 mM; Na azide 0.02%; D2O 10%; H2O 90%

sample_2: rotavirus VP4, [U-15N; U-13C; U-2H], 1 mM; NaPO4 20 mM; NaCl 10 mM; Na azide 0.02%; D2O 10%; H2O 90%

sample_3_1: rotavirus VP4, [U-15N]-Ile, 0.1 mM; NaPO4 20 mM; NaCl 10 mM; Na azide 0.02%; D2O 10%; H2O 90%

sample_3_2: rotavirus VP4, [U-15N]-Leu, 0.1 mM; NaPO4 20 mM; NaCl 10 mM; Na azide 0.02%; D2O 10%; H2O 90%

sample_3_3: rotavirus VP4, [U-15N]-Phe, 0.1 mM; NaPO4 20 mM; NaCl 10 mM; Na azide 0.02%; D2O 10%; H2O 90%

sample_3_4: rotavirus VP4, [U-15N]-Tyr, 0.1 mM; NaPO4 20 mM; NaCl 10 mM; Na azide 0.02%; D2O 10%; H2O 90%

sample_3_5: rotavirus VP4, [U-15N]-Val, 0.1 mM; NaPO4 20 mM; NaCl 10 mM; Na azide 0.02%; D2O 10%

sample_4: rotavirus VP4, [U-15N; U-13C], 1 mM; NaPO4 20 mM; NaCl 10 mM; Na azide 0.02%; D2O 10%; H2O 90%

sample_5: rotavirus VP4, [U-13C], 1 mM; NaPO4 20 mM; NaCl 10 mM; Na azide 0.02%; D2O 100%

sample_cond_1: pH: 7.0; temperature: 298 K; ionic strength: 0.030 M; pressure: 1 atm

Experiments:

NameSampleSample stateSample conditions
HSQCnot availablenot availablesample_cond_1
HNCAnot availablenot availablesample_cond_1
HN(CO)CAnot availablenot availablesample_cond_1
HNCACBnot availablenot availablesample_cond_1
HN(CO)CACBnot availablenot availablesample_cond_1
HNCOnot availablenot availablesample_cond_1
HN(CA)COnot availablenot availablesample_cond_1
HCCCONHnot availablenot availablesample_cond_1
HNHAnot availablenot availablesample_cond_1
HNHBnot availablenot availablesample_cond_1
3D 15N-separated TOCHSQCnot availablenot availablesample_cond_1
HCCH-TOCSYnot availablenot availablesample_cond_1
13C HSQCnot availablenot availablesample_cond_1
2D D2O-TOCSYnot availablenot availablesample_cond_1
3D 13C-separated NOESYnot availablenot availablesample_cond_1
3D 15N-separated NOEHSQCnot availablenot availablesample_cond_1
2D D2O-NOESYnot availablenot availablesample_cond_1

Software:

PROSA v3.7 - processing

XEASY v1.3.13 - data analysis

DYANA v1.5 - data analysis

TALOS - data analysis

CNS v1.0 - structure solution

NMR spectrometers:

  • Varian INOVA 750 MHz
  • Bruker AVANCE 600 MHz
  • Varian UNITY 500 MHz

Related Database Links:

PDB
GB AAA47345 AAK52093 AAQ22730 ACC94315 AEK32854
SP P12473
AlphaFold P12473 P12473

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks