BMRB Entry 51052

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51052

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Title:
Assignment of nsp3a-nucleoprotein complex of SARS-CoV-2
Deposition date:
2021-08-10
Original release date:
2022-01-20
Authors:
Mamigonian Bessa, Luiza; Camacho Zarco, Aldo; Guseva, Serafima; Salvi, Nicola; Blackledge, Martin
Citation:

Citation: Bessa, Luiza Mamigonian; Guseva, Serafima; Camacho-Zarco, Aldo; Salvi, Nicola; Maurin, Damien; Perez, Laura Marino; Botova, Maiia; Malki, Anas; Nanao, Max; Jensen, Malene Ringkjobing; Ruigrok, Rob; Blackledge, Martin. "The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a"  Sci. Adv. 8, eabm4034-eabm4034 (2022).
PubMed: 35044811

Assembly members:

Assembly members:
entity_1, polymer, 99 residues, 11255.68 Da.
entity_2, polymer, 114 residues, 12719.34 Da.
entity_3, polymer, 76 residues, 8066 Da.
entity_4, polymer, 76 residues, 8126 Da.
entity_5, polymer, 92 residues, 9601.60 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   Vector: pESPRIT

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GRRQGYKSVNITFELDERID KVLNEKCSAYTVELGTEVNE FACVVADAVIKTLQPVSELL TPLGIDLDEWSMATYYLFDE SGEFKLASHMYCSFYPPDE
entity_2: GAMAPTKVTFGDDTVIEVQG YKSVNITFELDERIDKVLNE KCSAYTVELGTEVNEFACVV ADAVIKTLQPVSELLTPLGI DLDEWSMATYYLFDESGEFK LASHMYCSFYPPDE
entity_3: GRRRNSSRNSTPGSSRGTSP ARMAGNGGDAALALLLLDRL NQLESKMSGKGQQQQGQTVT KKSAAEASKKPRQKRT
entity_4: GRRRNSSRNSTPGSSRGTSP ARMAGNGGDAALALLLLDRL NQLESKMFGKGQQQQGQTVT KKSAAEASKKPRQKRT
entity_5: GRRGSRGGSQASSRSSSRSR NSSRNSTPGSSRGTSPARMA GNGGDAALALLLLDRLNQLE SKMSGKGQQQQGQTVTKKSA AEASKKPRQKRT

Data sets:
Data typeCount
13C chemical shifts322
15N chemical shifts156
1H chemical shifts593

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1SARS-CoV-2 Nsp3, 16-1111
2SARS-CoV-2 Nsp3, 1-1112
3SARS-CoV-2 Nucleoprotein, 191-2633
4SARS-CoV-2 Nucleoprotein, 191-263 S235F4
5SARS-CoV-2 Nucleoprotein, 175-2635

Entities:

Entity 1, SARS-CoV-2 Nsp3, 16-111 99 residues - 11255.68 Da.

Represents residues 16-111 of SARS-CoV-2 Nsp3 with non-native GRR- N-terminal extension.

1   GLYARGARGGLNGLYTYRLYSSERVALASN
2   ILETHRPHEGLULEUASPGLUARGILEASP
3   LYSVALLEUASNGLULYSCYSSERALATYR
4   THRVALGLULEUGLYTHRGLUVALASNGLU
5   PHEALACYSVALVALALAASPALAVALILE
6   LYSTHRLEUGLNPROVALSERGLULEULEU
7   THRPROLEUGLYILEASPLEUASPGLUTRP
8   SERMETALATHRTYRTYRLEUPHEASPGLU
9   SERGLYGLUPHELYSLEUALASERHISMET
10   TYRCYSSERPHETYRPROPROASPGLU

Entity 2, SARS-CoV-2 Nsp3, 1-111 114 residues - 12719.34 Da.

Represents residues 1-111 of SARS-CoV-2 Nsp3 with non-native GAM- N-terminal extension

1   GLYALAMETALAPROTHRLYSVALTHRPHE
2   GLYASPASPTHRVALILEGLUVALGLNGLY
3   TYRLYSSERVALASNILETHRPHEGLULEU
4   ASPGLUARGILEASPLYSVALLEUASNGLU
5   LYSCYSSERALATYRTHRVALGLULEUGLY
6   THRGLUVALASNGLUPHEALACYSVALVAL
7   ALAASPALAVALILELYSTHRLEUGLNPRO
8   VALSERGLULEULEUTHRPROLEUGLYILE
9   ASPLEUASPGLUTRPSERMETALATHRTYR
10   TYRLEUPHEASPGLUSERGLYGLUPHELYS
11   LEUALASERHISMETTYRCYSSERPHETYR
12   PROPROASPGLU

Entity 3, SARS-CoV-2 Nucleoprotein, 191-263 76 residues - 8066 Da.

Represents residues 191-263 of SARS-CoV-2 Nucleoprotein with non-native GRR- N-terminal extension.

1   GLYARGARGARGASNSERSERARGASNSER
2   THRPROGLYSERSERARGGLYTHRSERPRO
3   ALAARGMETALAGLYASNGLYGLYASPALA
4   ALALEUALALEULEULEULEUASPARGLEU
5   ASNGLNLEUGLUSERLYSMETSERGLYLYS
6   GLYGLNGLNGLNGLNGLYGLNTHRVALTHR
7   LYSLYSSERALAALAGLUALASERLYSLYS
8   PROARGGLNLYSARGTHR

Entity 4, SARS-CoV-2 Nucleoprotein, 191-263 S235F 76 residues - 8126 Da.

Represents residues 191-263 of SARS-CoV-2 Nucleoprotein with non-native GRR- N-terminal extension. Contains S235F mutation present in the alpha variant of SARS-CoV-2

1   GLYARGARGARGASNSERSERARGASNSER
2   THRPROGLYSERSERARGGLYTHRSERPRO
3   ALAARGMETALAGLYASNGLYGLYASPALA
4   ALALEUALALEULEULEULEUASPARGLEU
5   ASNGLNLEUGLUSERLYSMETPHEGLYLYS
6   GLYGLNGLNGLNGLNGLYGLNTHRVALTHR
7   LYSLYSSERALAALAGLUALASERLYSLYS
8   PROARGGLNLYSARGTHR

Entity 5, SARS-CoV-2 Nucleoprotein, 175-263 92 residues - 9601.60 Da.

Represents residues 175-263 of SARS-CoV-2 Nucleoprotein with non-native GRR- N-terminal extension.

1   GLYARGARGGLYSERARGGLYGLYSERGLN
2   ALASERSERARGSERSERSERARGSERARG
3   ASNSERSERARGASNSERTHRPROGLYSER
4   SERARGGLYTHRSERPROALAARGMETALA
5   GLYASNGLYGLYASPALAALALEUALALEU
6   LEULEULEUASPARGLEUASNGLNLEUGLU
7   SERLYSMETSERGLYLYSGLYGLNGLNGLN
8   GLNGLYGLNTHRVALTHRLYSLYSSERALA
9   ALAGLUALASERLYSLYSPROARGGLNLYS
10   ARGTHR

Samples:

sample_1: SARS-CoV-2 Nsp3 1-111, [U-13C; U-15N; U-2H], 320 uM; SARS-CoV-2 N 175-263 640 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM; D2O, [U-99% 2H], 10%

sample_2: SARS-CoV-2 Nucleoprotein 175-263, [U-13C; U-15N; U-2H], 600 uM; SARS-CoV-2 Nsp3 1-111 1200 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM; D2O, [U-99% 2H], 10%

sample_3: SARS-CoV-2 Nsp3 16-111, [U-99% 13C; U-99% 15N], 200 uM; SARS-CoV-2 Nucleoprotein 191-263 200 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM; D2O, [U-99% 2H], 10%

sample_4: SARS-CoV-2 Nsp3 16-111, [U-99% 13C; U-99% 15N], 500 uM; SARS-CoV-2 Nucleoprotein 191-263 550 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM; D2O, [U-99% 2H], 10%

sample_5: SARS-CoV-2 Nucleoprotein 191-263, [U-99% 13C; U-99% 15N], 500 uM; SARS-CoV-2 Nsp3 16-111 550 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM; D2O, [U-99% 2H], 10%

sample_6: SARS-CoV-2 Nucleoprotein 191-263 S235F, [U-99% 13C; U-99% 15N], 500 uM; SARS-CoV-2 Nsp3 16-111 550 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM; D2O, [U-99% 2H], 10%

sample_7: SARS-CoV-2 Nsp3 16-111 500 uM; SARS-CoV-2 Nucleoprotein 191-263 500 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM; D2O, [U-99% 2H], 10%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298.13 K

Experiments:

NameSampleSample stateSample conditions
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D (H)CCH-TOCSYsample_4isotropicsample_conditions_1
2D 1H-15N HSQCsample_4isotropicsample_conditions_1
3D 1H-15N NOESYsample_4isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_4isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
2D 1H-1H NOESYsample_7isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HN(CO)CACBsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HN(CA)COsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_5isotropicsample_conditions_1
3D 1H-15N NOESYsample_5isotropicsample_conditions_1
3D HCCH-TOCSYsample_5isotropicsample_conditions_1
3D (H)CCH-TOCSYsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
3D HNCAsample_6isotropicsample_conditions_1
3D HN(CO)CAsample_6isotropicsample_conditions_1
2D 1H-15N HSQCsample_6isotropicsample_conditions_1
2D 1H-13C HSQCsample_6isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_6isotropicsample_conditions_1
3D 1H-15N TOCSY-HSQCsample_5isotropicsample_conditions_1

Software:

TOPSPIN v3.5 and 4.1 - collection

NMRFAM-SPARKY v1.3 - chemical shift assignment, data analysis, peak picking

CcpNMR Analysis v2.5 - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III 700 MHz
  • Bruker AVANCE III 850 MHz
  • Bruker AVANCE III 950 MHz
  • Bruker AVANCE NEO 950 MHz

Related Database Links:

NCBI P0C6X7 P0C6X7 P0DTC9 P0DTC9 P0DTC9

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