BMRB Entry 30008

Name: Quantitative characterization of configurational space sampled by HIV-1 nucleocapsid using solution NMR and X-ray scattering
Published: 2016-06-17

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PDB ID: 5i1r
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30008
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	125
15N chemical shifts	42
1H chemical shifts	42

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_ZN	2
3	entity_ZN	2

Entities:

Entity 1, entity_1 55 residues - 6442.522 Da.

1

MET

GLN

ARG

GLY

ASN

PHE

ARG

ASN

GLN

ARG

2

LYS

ILE

VAL

LYS

CYS

PHE

ASN

CYS

GLY

LYS

3

GLU

GLY

HIS

THR

ALA

ARG

ASN

CYS

ARG

ALA

4

PRO

ARG

LYS

GLY

CYS

TRP

LYS

CYS

GLY

5

LYS

GLU

GLY

HIS

GLN

MET

LYS

ASP

CYS

THR

6

GLU

ARG

GLN

ALA

ASN

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
2D ARTSY	sample_2	anisotropic	sample_conditions_1
3D Quntitaive HNCO - NC'	sample_2	anisotropic	sample_conditions_1
3D Quntitaive HNCO - CaC'	sample_2	anisotropic	sample_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