BMRB Entry 18980

Title:
NMR solution structure of HIV-1 nucleocapsid protein in complex with an inhibitor displaying a 2 inhibitors:1 NC stoichiometry
Deposition date:
2013-01-28
Original release date:
2013-02-21
Authors:
Goudreau, Nathalie; Hucke, Oliver
Citation:

Citation: Goudreau, Nathalie; Hucke, Oliver; Faucher, Anne-Marie; Grand-Maitre, Chantal; Lepage, Olivier; Bonneau, Pierre; Mason, Stephen; Titolo, Steve. "Discovery and structural characterization of a new inhibitor series of HIV-1 nucleocapsid function: NMR solution structure determination of a ternary complex involving a 2:1 inhibitor/NC stoichiometry."  J. Mol. Biol. 425, 1982-1998 (2013).
PubMed: 23485336

Assembly members:

Assembly members:
entity_1, polymer, 55 residues, 6368.487 Da.
entity_ZN, non-polymer, 65.409 Da.
(3E)-3-{(2Z)-[(5Z)-5-(furan-2-ylmethylidene)-4-oxo-1,3-thiazolidin-2-ylidene]hydrazinylidene}-2-oxo-2,3-dihydro-1H-indole-5-sulfonic acid, non-polymer, 418.404 Da.

Natural source:

Natural source:   Common Name: HIV-1   Taxonomy ID: 11676   Superkingdom: Viruses   Kingdom: not available   Genus/species: Lentivirus HIV-1

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-11a

Entity Sequences (FASTA):

Data sets:
Data typeCount
13C chemical shifts154
15N chemical shifts61
1H chemical shifts391

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1NC inhibitor 31
2ZINC ION_12
3ZINC ION_22
43,6-BIS{3-[(2R)-(2-ETHYLPIPERIDINO)]PROPIONAMIDO}ACRIDINE_13
53,6-BIS{3-[(2R)-(2-ETHYLPIPERIDINO)]PROPIONAMIDO}ACRIDINE_23

Entities:

Entity 1, NC inhibitor 3 55 residues - 6368.487 Da.

1   ILEGLNLYSGLYASNPHEARGASNGLNARG
2   LYSTHRVALLYSCYSPHEASNCYSGLYLYS
3   GLUGLYHISILEALALYSASNCYSARGALA
4   PROARGLYSLYSGLYCYSTRPLYSCYSGLY
5   LYSGLUGLYHISGLNMETLYSASPCYSTHR
6   GLUARGGLNALAASN

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Entity 3, 3,6-BIS{3-[(2R)-(2-ETHYLPIPERIDINO)]PROPIONAMIDO}ACRIDINE_1 - C16 H10 N4 O6 S2 - 418.404 Da.

1   1HF

Samples:

sample_1: NC inhibitor 3, [U-100% 13C; U-100% 15N], 250 ± 50 uM; 3,6-BIS{3-[(2R)-(2-ETHYLPIPERIDINO)]PROPIONAMIDO}ACRIDINE 500 ± 10 uM; sodium phosphate 25 ± 10 mM

sample_conditions_1: ionic strength: 0.025 M; pH: 6.5; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1

Software:

AMBER v8.0, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure solution

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAC77511 BAC77512 BAF34641 BAO09940
EMBL CBI61180 CBI61183 CBI61184 CBI61185 CBI61186
GB AAA44987 AAB08996 AAB60571 AAB82953 AAB82955
SP P12493 P12497
AlphaFold P12497 P12493

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