BMRB Entry 30035

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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

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Title:
Dimerization interface of the noncrystalline HIV-1 capsid protein lattice from solid state NMR spectroscopy of tubular assemblies
Deposition date:
2016-03-14
Original release date:
2016-06-20
Authors:
Bayro, M.; Tycko, R.
Citation:

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).
PubMed: 27298207

Assembly members:

Assembly members:
Capsid protein p24, polymer, 231 residues, 25630.426 Da.

Natural source:

Natural source:   Common Name: HIV-1   Taxonomy ID: 11698   Superkingdom: retrovirus   Kingdom: lentivirus   Genus/species: Human Immunodeficiency virus 1 not available

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Capsid protein p24: PIVQNLQGQMVHQAISPRTL NAWVKVVEEKAFSPEVIPMF SALSEGATPQDLNTMLNTVG GHQAAMQMLKETINEEAAEW DRLHPVHAGPIAPGQMREPR GSDIAGTTSTLQEQIGWMTH NPPIPVGEIYKRWIILGLNK IVRMYSPTSILDIRQGPKEP FRDYVDRFYKTLRAEQASQE VKNWMTETLLVQNANPDCKT ILKALGPGATLEEMMTACQG VGGPGHKARVL

Data sets:
Data typeCount
13C chemical shifts603
15N chemical shifts188

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, chain 11
2entity_1, chain 21

Entities:

Entity 1, entity_1, chain 1 231 residues - 25630.426 Da.

1   PROILEVALGLNASNLEUGLNGLYGLNMET
2   VALHISGLNALAILESERPROARGTHRLEU
3   ASNALATRPVALLYSVALVALGLUGLULYS
4   ALAPHESERPROGLUVALILEPROMETPHE
5   SERALALEUSERGLUGLYALATHRPROGLN
6   ASPLEUASNTHRMETLEUASNTHRVALGLY
7   GLYHISGLNALAALAMETGLNMETLEULYS
8   GLUTHRILEASNGLUGLUALAALAGLUTRP
9   ASPARGLEUHISPROVALHISALAGLYPRO
10   ILEALAPROGLYGLNMETARGGLUPROARG
11   GLYSERASPILEALAGLYTHRTHRSERTHR
12   LEUGLNGLUGLNILEGLYTRPMETTHRHIS
13   ASNPROPROILEPROVALGLYGLUILETYR
14   LYSARGTRPILEILELEUGLYLEUASNLYS
15   ILEVALARGMETTYRSERPROTHRSERILE
16   LEUASPILEARGGLNGLYPROLYSGLUPRO
17   PHEARGASPTYRVALASPARGPHETYRLYS
18   THRLEUARGALAGLUGLNALASERGLNGLU
19   VALLYSASNTRPMETTHRGLUTHRLEULEU
20   VALGLNASNALAASNPROASPCYSLYSTHR
21   ILELEULYSALALEUGLYPROGLYALATHR
22   LEUGLUGLUMETMETTHRALACYSGLNGLY
23   VALGLYGLYPROGLYHISLYSALAARGVAL
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:

NameSampleSample stateSample conditions
13C-13C 2D correlationsample_1isotropicsample_conditions_1
NCACX 2D correlationsample_1isotropicsample_conditions_1
NCOCX 2D correlationsample_1isotropicsample_conditions_1
13C-13C 2D correlationsample_2isotropicsample_conditions_1
13C-13C 2D correlationsample_3isotropicsample_conditions_1
NCACX 2D correlationsample_3isotropicsample_conditions_1
LGCP 1H-13C 1D buildupsample_4isotropicsample_conditions_1
LGCP 1H-15N 1D buildupsample_4isotropicsample_conditions_1
Intermolecular REDORsample_4isotropicsample_conditions_1
Side-chain/backbone REDORsample_5isotropicsample_conditions_1
BroBaRR 13C-13C buildupsample_1isotropicsample_conditions_1
Vector angle Trp Ca-N/Cd1-Ne1sample_3isotropicsample_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