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
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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 PubMed: 23485336
Deposition date: 2013-01-28 Original release date: 2013-02-21
Authors: Goudreau, Nathalie; Hucke, Oliver
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).
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: Common Name: HIV-1 Taxonomy ID: 11676 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus HIV-1
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: IQKGNFRNQRKTVKCFNCGK
EGHIAKNCRAPRKKGCWKCG
KEGHQMKDCTERQAN
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 154 |
| 15N chemical shifts | 61 |
| 1H chemical shifts | 391 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | NC inhibitor 3 | 1 |
| 2 | ZINC ION_1 | 2 |
| 3 | ZINC ION_2 | 2 |
| 4 | 3,6-BIS{3-[(2R)-(2-ETHYLPIPERIDINO)]PROPIONAMIDO}ACRIDINE_1 | 3 |
| 5 | 3,6-BIS{3-[(2R)-(2-ETHYLPIPERIDINO)]PROPIONAMIDO}ACRIDINE_2 | 3 |
Entities:
Entity 1, NC inhibitor 3 55 residues - 6368.487 Da.
| 1 | ILE | GLN | LYS | GLY | ASN | PHE | ARG | ASN | GLN | ARG | ||||
| 2 | LYS | THR | VAL | LYS | CYS | PHE | ASN | CYS | GLY | LYS | ||||
| 3 | GLU | GLY | HIS | ILE | ALA | LYS | ASN | CYS | ARG | ALA | ||||
| 4 | PRO | ARG | LYS | 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, 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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_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 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts