BMRB Entry 30008

Title:
Quantitative characterization of configurational space sampled by HIV-1 nucleocapsid using solution NMR and X-ray scattering
Deposition date:
2016-02-05
Original release date:
2016-06-17
Authors:
Deshmukh, L.; Schwieters, C.; Grishaev, A.; Clore, G.
Citation:

Citation: Deshmukh, L.; Schwieters, C.; Grishaev, A.; Clore, G.. "Quantitative characterization of configurational space sampled by HIV-1 nucleocapsid using solution NMR, X-ray scattering and protein engineering"  Chemphyschem 17, 1548-1552 (2016).
PubMed: 26946052

Assembly members:

Assembly members:
Nucleocapsid protein p7, polymer, 55 residues, 6442.522 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: HIV-1   Taxonomy ID: 11706   Superkingdom: Viruses   Kingdom: not available   Genus/species: Retroviruses HIV-1

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET11a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Nucleocapsid protein p7: MQRGNFRNQRKIVKCFNCGK EGHTARNCRAPRKKGCWKCG KEGHQMKDCTERQAN

Data sets:
Data typeCount
13C chemical shifts125
15N chemical shifts42
1H chemical shifts42

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_ZN2
3entity_ZN2

Entities:

Entity 1, entity_1 55 residues - 6442.522 Da.

1   METGLNARGGLYASNPHEARGASNGLNARG
2   LYSILEVALLYSCYSPHEASNCYSGLYLYS
3   GLUGLYHISTHRALAARGASNCYSARGALA
4   PROARGLYSLYSGLYCYSTRPLYSCYSGLY
5   LYSGLUGLYHISGLNMETLYSASPCYSTHR
6   GLUARGGLNALAASN

Entity 2, entity_ZN - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: Dithiothreitol 1 mM; Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), [U-13C; U-15N; U-2H], 0.2 mM; sodium chloride 50 mM; sodium phosphate 20 mM; zinc chloride 0.1 mM; H2O 93%; D2O 7%

sample_2: Dithiothreitol 1 mM; Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), [U-13C; U-15N; U-2H], 0.2 mM; neutral bicelles 5%; sodium chloride 50 mM; sodium phosphate 20 mM; zinc chloride 0.1 mM; H2O 93%; D2O 7%

sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
2D ARTSYsample_2anisotropicsample_conditions_1
3D Quntitaive HNCO - NC'sample_2anisotropicsample_conditions_1
3D Quntitaive HNCO - CaC'sample_2anisotropicsample_conditions_1

Software:

Analysis v2.2.2, W. F. Vranken, W. Boucher, T. J. Stevens, R. H. Fogh, A. Pajon, M. Llinas, E. L. Ulrich, J. L. Markley, J. Ionides, E. D. Laue - chemical shift assignment, peak picking

Xplor-NIH v2.41, C. D. Schwieters, J. J. Kuszewski, N. Tjandra, G. M. Clore - refinement

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 800 MHz

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