BMRB Entry 18980

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18980
MolProbity Validation Chart

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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):

Entity Sequences (FASTA):
entity_1: IQKGNFRNQRKTVKCFNCGK EGHIAKNCRAPRKKGCWKCG KEGHQMKDCTERQAN

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

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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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 P12493 P12497

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CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks