BMRB Entry 51456

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51456

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Title:
Near complete backbone assignment of a C145A variant of the main protease from SARS-CoV-2 complexed with native N-terminal substrate SAVLQSGFRK
Deposition date:
2022-05-20
Original release date:
2022-09-13
Authors:
Robertson, Angus; Ying, Jinfa; Bax, Adriaan
Citation:

Citation: Robertson, Angus; Ying, Jinfa; Bax, Adriaan. "NMR Observation of Sulfhydryl Signals in SARS-CoV-2 Main Protease Aids Structural Studies"  Chembiochem ., e202200471-e202200471 (2022).
PubMed: 35972230

Assembly members:

Assembly members:
entity_1, polymer, 306 residues, 68000 Da.
entity_2, polymer, 11 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: pET-24a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SGFRKMAFPSGKVEGCMVQV TCGTTTLNGLWLDDVVYCPR HVICTSEDMLNPNYEDLLIR KSNHNFLVQAGNVQLRVIGH SMQNCVLKLKVDTANPKTPK YKFVRIQPGQTFSVLACYNG SPSGVYQCAMRPNFTIKGSF LNGSAGSVGFNIDYDCVSFC YMHHMELPTGVHAGTDLEGN FYGPFVDRQTAQAAGTDTTI TVNVLAWLYAAVINGDRWFL NRFTTTLNDFNLVAMKYNYE PLTQDHVDILGPLSAQTGIA VLDMCASLKELLQNGMNGRT ILGSALLEDEFTPFDVVRQC SGVTFQ
entity_2: XSAVLQSGFRK

Data sets:
Data typeCount
13C chemical shifts765
15N chemical shifts286
1H chemical shifts296

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1SARS-CoV-2 main protease, chain 11
2SARS-CoV-2 main protease, chain 21
3substrate, chain 12
4substrate, chain 22

Entities:

Entity 1, SARS-CoV-2 main protease, chain 1 306 residues - 68000 Da.

C145A variant of SARS CoV 2 main protease.

1   SERGLYPHEARGLYSMETALAPHEPROSER
2   GLYLYSVALGLUGLYCYSMETVALGLNVAL
3   THRCYSGLYTHRTHRTHRLEUASNGLYLEU
4   TRPLEUASPASPVALVALTYRCYSPROARG
5   HISVALILECYSTHRSERGLUASPMETLEU
6   ASNPROASNTYRGLUASPLEULEUILEARG
7   LYSSERASNHISASNPHELEUVALGLNALA
8   GLYASNVALGLNLEUARGVALILEGLYHIS
9   SERMETGLNASNCYSVALLEULYSLEULYS
10   VALASPTHRALAASNPROLYSTHRPROLYS
11   TYRLYSPHEVALARGILEGLNPROGLYGLN
12   THRPHESERVALLEUALACYSTYRASNGLY
13   SERPROSERGLYVALTYRGLNCYSALAMET
14   ARGPROASNPHETHRILELYSGLYSERPHE
15   LEUASNGLYSERALAGLYSERVALGLYPHE
16   ASNILEASPTYRASPCYSVALSERPHECYS
17   TYRMETHISHISMETGLULEUPROTHRGLY
18   VALHISALAGLYTHRASPLEUGLUGLYASN
19   PHETYRGLYPROPHEVALASPARGGLNTHR
20   ALAGLNALAALAGLYTHRASPTHRTHRILE
21   THRVALASNVALLEUALATRPLEUTYRALA
22   ALAVALILEASNGLYASPARGTRPPHELEU
23   ASNARGPHETHRTHRTHRLEUASNASPPHE
24   ASNLEUVALALAMETLYSTYRASNTYRGLU
25   PROLEUTHRGLNASPHISVALASPILELEU
26   GLYPROLEUSERALAGLNTHRGLYILEALA
27   VALLEUASPMETCYSALASERLEULYSGLU
28   LEULEUGLNASNGLYMETASNGLYARGTHR
29   ILELEUGLYSERALALEULEUGLUASPGLU
30   PHETHRPROPHEASPVALVALARGGLNCYS
31   SERGLYVALTHRPHEGLN

Entity 2, substrate, chain 1 11 residues - Formula weight is not available

Peptide includes an N-terminal acetylation

1   ACESERALAVALLEUGLNSERGLYPHEARG
2   LYS

Samples:

sample_1: Main protease of SARS-CoV-2 (C145A variant), [U-13C; U-15N; U-2H], 500 uM; nsp5 N-terminal cleavage sequence 5 mM; sodium phosphate 10 mM; TCEP 0.5 mM; DSS 0.3 mM; D2O 3%

sample_conditions_1: ionic strength: 38 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCBsample_1isotropicsample_conditions_1
3D 15N-separated NOESYsample_1isotropicsample_conditions_1

Software:

NMRFAM-SPARKY - chemical shift assignment, data analysis, peak picking

CYANA - chemical shift assignment

NMRPipe - data analysis, peak picking

TOPSPIN vV3 & V4 - collection

nmrglue - data analysis

NMR spectrometers:

  • Bruker AVANCE NEO 900 MHz
  • Bruker AVANCE III 800 MHz

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