BMRB Entry 34748

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34748
MolProbity Validation Chart

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Title:
Solution NMR structure of full-length Nsp1 from SARS-CoV-2
Deposition date:
2022-08-08
Original release date:
2022-12-09
Authors:
Wang, Y.; Kirkpatrick, J.; Carlomagno, T.
Citation:

Citation: Wang, Y.; Kirkpatrick, J.; zur Lage, S.; Carlomagno, T.. "Structural insights into the activity regulation of full-length non-structural protein 1 from SARS-CoV-2"  .

Assembly members:

Assembly members:
entity_1, polymer, 182 residues, 19929.414 Da.

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 BL21   Vector: pETM11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GAMESLVPGFNEKTHVQLSL PVLQVRDVLVRGFGDSVEEV LSEARQHLKDGTCGLVEVEK GVLPQLEQPYVFIKRSDART APHGHVMVELVAELEGIQYG RSGETLGVLVPHVGEIPVAY RKVLLRKNGNKGAGGHSYGA DLKSFDLGDELGTDPYEDFQ ENWNTKHSSGVTRELMRELN GG

Data sets:
Data typeCount
13C chemical shifts803
15N chemical shifts187
1H chemical shifts1269

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 182 residues - 19929.414 Da.

1   GLYALAMETGLUSERLEUVALPROGLYPHE
2   ASNGLULYSTHRHISVALGLNLEUSERLEU
3   PROVALLEUGLNVALARGASPVALLEUVAL
4   ARGGLYPHEGLYASPSERVALGLUGLUVAL
5   LEUSERGLUALAARGGLNHISLEULYSASP
6   GLYTHRCYSGLYLEUVALGLUVALGLULYS
7   GLYVALLEUPROGLNLEUGLUGLNPROTYR
8   VALPHEILELYSARGSERASPALAARGTHR
9   ALAPROHISGLYHISVALMETVALGLULEU
10   VALALAGLULEUGLUGLYILEGLNTYRGLY
11   ARGSERGLYGLUTHRLEUGLYVALLEUVAL
12   PROHISVALGLYGLUILEPROVALALATYR
13   ARGLYSVALLEULEUARGLYSASNGLYASN
14   LYSGLYALAGLYGLYHISSERTYRGLYALA
15   ASPLEULYSSERPHEASPLEUGLYASPGLU
16   LEUGLYTHRASPPROTYRGLUASPPHEGLN
17   GLUASNTRPASNTHRLYSHISSERSERGLY
18   VALTHRARGGLULEUMETARGGLULEUASN
19   GLYGLY

Samples:

sample_1: Nsp1, [U-13C; U-15N], 600 ± 100 uM; sodium phosphate 50 ± 5 mM; sodium chloride 200 ± 10 mM; DTT 2 ± 0.1 mM; EDTA 2 ± 0.1 mM; sodium azide 0.01 ± 0.001 % w/v; D2O, [U-2H], 10 ± 0.5 % v/v

sample_2: Nsp1, [U-10% 13C; U-100% 15N], 500 ± 100 uM; sodium phosphate 50 ± 5 mM; sodium chloride 200 ± 10 mM; DTT 2 ± 0.1 mM; EDTA 2 ± 0.1 mM; sodium azide 0.01 ± 0.001 % w/v; D2O, [U-2H], 10 ± 0.5 % v/v

sample_3: Nsp1, [U-10% 13C; U-100% 15N], 500 ± 100 uM; sodium phosphate 50 ± 5 mM; sodium chloride 200 ± 10 mM; DTT 2 ± 0.1 mM; EDTA 2 ± 0.1 mM; sodium azide 0.01 ± 0.001 % w/w; D2O, [U-2H], 10 ± 0.5 % v/v; Pf1 phage 12 ± 1 mg/mL

sample_conditions_1: ionic strength: 560 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(COCA)CBsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HA(CO)NHsample_1isotropicsample_conditions_1
3D HC(C)H-TOCSY (aromatics)sample_1isotropicsample_conditions_1
3D (H)CCH-TOCSY (aromatics)sample_1isotropicsample_conditions_1
2D (HB)CB(CGCD)HDsample_1isotropicsample_conditions_1
2D (HB)CB(CGCDCE)HEsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D CT 1H-13C HSQC (aliphatics)sample_1isotropicsample_conditions_1
2D CT 1H-13C HSQC (aromatics)sample_1isotropicsample_conditions_1
2D CT 1H-13C HSQC (methyls)sample_2isotropicsample_conditions_1
3D NOESY-15N HSQCsample_1isotropicsample_conditions_1
3D NOESY-13C HSQCsample_1isotropicsample_conditions_1
CLEANEXsample_2isotropicsample_conditions_1
2D SCT 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_2isotropicsample_conditions_1
2D IPAP 1H-15N HSQCsample_2isotropicsample_conditions_1
2D SCT 1H-15N HSQCsample_3anisotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_3anisotropicsample_conditions_1
2D IPAP 1H-15N HSQCsample_3anisotropicsample_conditions_1

Software:

TopSpin v3.2, Bruker Biospin - collection

NMRPipe v10.1, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CcpNmr Analysis v2.4, CCPN - chemical shift assignment, data analysis, peak picking

ARIA v2.3, Linge, O'Donoghue and Nilges - structure calculation

CNS v1.21, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

NMR spectrometers:

  • Bruker AVANCE III HD 600 MHz
  • Bruker AVANCE III HD 850 MHz

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