BMRB Entry 30035
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30035
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: Dimerization interface of the noncrystalline HIV-1 capsid protein lattice from solid state NMR spectroscopy of tubular assemblies PubMed: 27298207
Deposition date: 2016-03-14 Original release date: 2016-06-20
Authors: Bayro, M.; Tycko, R.
Citation: Bayro, M.; Tycko, R.. "Structure of the Dimerization Interface in the Mature HIV-1 Capsid Protein Lattice from Solid State NMR of Tubular Assemblies" J. Am. Chem. Soc. 138, 8538-8546 (2016).
Assembly members:
Capsid protein p24, polymer, 231 residues, 25630.426 Da.
Natural source: Common Name: HIV-1 Taxonomy ID: 11698 Superkingdom: retrovirus Kingdom: lentivirus Genus/species: Human Immunodeficiency virus 1 not available
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Capsid protein p24: PIVQNLQGQMVHQAISPRTL
NAWVKVVEEKAFSPEVIPMF
SALSEGATPQDLNTMLNTVG
GHQAAMQMLKETINEEAAEW
DRLHPVHAGPIAPGQMREPR
GSDIAGTTSTLQEQIGWMTH
NPPIPVGEIYKRWIILGLNK
IVRMYSPTSILDIRQGPKEP
FRDYVDRFYKTLRAEQASQE
VKNWMTETLLVQNANPDCKT
ILKALGPGATLEEMMTACQG
VGGPGHKARVL
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 603 |
| 15N chemical shifts | 188 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1, chain 1 | 1 |
| 2 | entity_1, chain 2 | 1 |
Entities:
Entity 1, entity_1, chain 1 231 residues - 25630.426 Da.
| 1 | PRO | ILE | VAL | GLN | ASN | LEU | GLN | GLY | GLN | MET | ||||
| 2 | VAL | HIS | GLN | ALA | ILE | SER | PRO | ARG | THR | LEU | ||||
| 3 | ASN | ALA | TRP | VAL | LYS | VAL | VAL | GLU | GLU | LYS | ||||
| 4 | ALA | PHE | SER | PRO | GLU | VAL | ILE | PRO | MET | PHE | ||||
| 5 | SER | ALA | LEU | SER | GLU | GLY | ALA | THR | PRO | GLN | ||||
| 6 | ASP | LEU | ASN | THR | MET | LEU | ASN | THR | VAL | GLY | ||||
| 7 | GLY | HIS | GLN | ALA | ALA | MET | GLN | MET | LEU | LYS | ||||
| 8 | GLU | THR | ILE | ASN | GLU | GLU | ALA | ALA | GLU | TRP | ||||
| 9 | ASP | ARG | LEU | HIS | PRO | VAL | HIS | ALA | GLY | PRO | ||||
| 10 | ILE | ALA | PRO | GLY | GLN | MET | ARG | GLU | PRO | ARG | ||||
| 11 | GLY | SER | ASP | ILE | ALA | GLY | THR | THR | SER | THR | ||||
| 12 | LEU | GLN | GLU | GLN | ILE | GLY | TRP | MET | THR | HIS | ||||
| 13 | ASN | PRO | PRO | ILE | PRO | VAL | GLY | GLU | ILE | TYR | ||||
| 14 | LYS | ARG | TRP | ILE | ILE | LEU | GLY | LEU | ASN | LYS | ||||
| 15 | ILE | VAL | ARG | MET | TYR | SER | PRO | THR | SER | ILE | ||||
| 16 | LEU | ASP | ILE | ARG | GLN | GLY | PRO | LYS | GLU | PRO | ||||
| 17 | PHE | ARG | ASP | TYR | VAL | ASP | ARG | PHE | TYR | LYS | ||||
| 18 | THR | LEU | ARG | ALA | GLU | GLN | ALA | SER | GLN | GLU | ||||
| 19 | VAL | LYS | ASN | TRP | MET | THR | GLU | THR | LEU | LEU | ||||
| 20 | VAL | GLN | ASN | ALA | ASN | PRO | ASP | CYS | LYS | THR | ||||
| 21 | ILE | LEU | LYS | ALA | LEU | GLY | PRO | GLY | ALA | THR | ||||
| 22 | LEU | GLU | GLU | MET | MET | THR | ALA | CYS | GLN | GLY | ||||
| 23 | VAL | GLY | GLY | PRO | GLY | HIS | LYS | ALA | ARG | VAL | ||||
| 24 | LEU |
Samples:
sample_1: Capsid protein, [U-15N; 13C-Met and U-15N], 15 mM; H2O 100%
sample_2: Capsid protein, [2-13C-glycerol; U-15N], 15 mM; H2O 100%
sample_3: Capsid protein, [2-13C-glycerol, U-15N; unlabeled Tyr and Phe], 15 mM; H2O 100%
sample_4: Capsid protein-1, [Methyl-13C-Met], 7.5 mM; Capsid protein-2, [15N-indole], 7.5 mM; H2O 100%
sample_5: Capsid protein, [Methyl-13C-Met, 2-13C-indole, U-15N], 15 mM; H2O 100%
sample_conditions_1: ionic strength: 1 M; pH: 8.0; pressure: 1 atm; temperature: 278 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 13C-13C 2D correlation | sample_1 | isotropic | sample_conditions_1 |
| NCACX 2D correlation | sample_1 | isotropic | sample_conditions_1 |
| NCOCX 2D correlation | sample_1 | isotropic | sample_conditions_1 |
| 13C-13C 2D correlation | sample_2 | isotropic | sample_conditions_1 |
| 13C-13C 2D correlation | sample_3 | isotropic | sample_conditions_1 |
| NCACX 2D correlation | sample_3 | isotropic | sample_conditions_1 |
| LGCP 1H-13C 1D buildup | sample_4 | isotropic | sample_conditions_1 |
| LGCP 1H-15N 1D buildup | sample_4 | isotropic | sample_conditions_1 |
| Intermolecular REDOR | sample_4 | isotropic | sample_conditions_1 |
| Side-chain/backbone REDOR | sample_5 | isotropic | sample_conditions_1 |
| BroBaRR 13C-13C buildup | sample_1 | isotropic | sample_conditions_1 |
| Vector angle Trp Ca-N/Cd1-Ne1 | sample_3 | isotropic | sample_conditions_1 |
Software:
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
SPARKY, Goddard - chemical shift assignment, peak picking
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation
NMR spectrometers:
- Varian Infinity 600 MHz
- Varian Infinity 750 MHz