BMRB Entry 51268

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51268

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Title:
Backbone chemical shift assignment of the SARS-CoV-2 receptor binding domain
Deposition date:
2022-01-12
Original release date:
2022-07-14
Authors:
Creutznacher, Robert; Peters, Thomas
Citation:

Citation: Creutznacher, Robert; Maass, Thorben; Veselkova, Barbora; Ssebyatika, George; Krey, Thomas; Empting, Martin; Tautz, Norbert; Frank, Martin; Kolbel, Knut; Uetrecht, Charlotte; Peters, Thomas. "NMR Experiments Provide Insights into Ligand-Binding to the SARS-CoV-2 Spike Protein Receptor-Binding Domain"  J. Am. Chem. Soc. 144, 13060-13065 (2022).
PubMed: 35830336

Assembly members:

Assembly members:
entity_1, polymer, 225 residues, Formula weight is not available

Natural source:

Natural source:   Common Name: SARS-CoV-2   Taxonomy ID: 2697049   Superkingdom: Viruses   Kingdom: not available   Genus/species: Betacoronavirus HCoV-SARS

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pMalC2x

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPRVQPTESIVRFPNITNLC PFGEVFNATRFASVYAWNRK RISNCVADYSVLYNSASFST FKCYGVSPTKLNDLCFTNVY ADSFVIRGDEVRQIAPGQTG KIADYNYKLPDDFTGCVIAW NSNNLDSKVGGNYNYLYRLF RKSNLKPFERDISTEIYQAG STPCNGVEGFNCYFPLQSYG FQPTNGVGYQPYRVVVLSFE LLHAPATVCGPKKSTNLVKN KSVNF

Data sets:
Data typeCount
13C chemical shifts604
15N chemical shifts197
1H chemical shifts197

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1RBD1

Entities:

Entity 1, RBD 225 residues - Formula weight is not available

Residues 1-2 ("GP") belong to a proteolytic cleavage site and are not present in the native SARS-CoV-2 spike protein.

1   GLYPROARGVALGLNPROTHRGLUSERILE
2   VALARGPHEPROASNILETHRASNLEUCYS
3   PROPHEGLYGLUVALPHEASNALATHRARG
4   PHEALASERVALTYRALATRPASNARGLYS
5   ARGILESERASNCYSVALALAASPTYRSER
6   VALLEUTYRASNSERALASERPHESERTHR
7   PHELYSCYSTYRGLYVALSERPROTHRLYS
8   LEUASNASPLEUCYSPHETHRASNVALTYR
9   ALAASPSERPHEVALILEARGGLYASPGLU
10   VALARGGLNILEALAPROGLYGLNTHRGLY
11   LYSILEALAASPTYRASNTYRLYSLEUPRO
12   ASPASPPHETHRGLYCYSVALILEALATRP
13   ASNSERASNASNLEUASPSERLYSVALGLY
14   GLYASNTYRASNTYRLEUTYRARGLEUPHE
15   ARGLYSSERASNLEULYSPROPHEGLUARG
16   ASPILESERTHRGLUILETYRGLNALAGLY
17   SERTHRPROCYSASNGLYVALGLUGLYPHE
18   ASNCYSTYRPHEPROLEUGLNSERTYRGLY
19   PHEGLNPROTHRASNGLYVALGLYTYRGLN
20   PROTYRARGVALVALVALLEUSERPHEGLU
21   LEULEUHISALAPROALATHRVALCYSGLY
22   PROLYSLYSSERTHRASNLEUVALLYSASN
23   LYSSERVALASNPHE

Samples:

sample_1: SARS-CoV-2 receptor binding domain, [U-13C; U-15N; U-2H], 390 uM; DSS, [U-2H], 500 uM; sodium chloride 10 mM; sodium phosphate 20 mM

sample_conditions_1: ionic strength: 30 mM; pH: 6.2; pressure: 1 atm; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1

Software:

CcpNMR v2.4 - chemical shift assignment, peak picking

TOPSPIN v3.6 - collection, processing

NMR spectrometers:

  • Bruker AVANCE III 600 MHz

Related Database Links:

NCBI YP_009724390.1

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