BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17307

Title: NMR Structure of the monomeric mutant C-terminal domain of HIV-1 Capsid in complex with stapled peptide Inhibitor   PubMed: 18417468

Deposition date: 2010-11-18 Original release date: 2010-12-16

Authors: Bhattacharya, Shibani; Zhang, Hongtao; Debnath, Asim; Cowburn, David

Citation: Bhattacharya, Shibani; Zhang, Hongtao; Debnath, Asim; Cowburn, David. "Solution structure of a hydrocarbon stapled peptide inhibitor in complex with monomeric C-terminal domain of HIV-1 capsid."  J. Biol. Chem. 283, 16247-16278 (2008).

Assembly members:
Capsid_protein_p24, polymer, 105 residues, Formula weight is not available
NYAD-13_Peptide_Inhibitor, polymer, 14 residues, Formula weight is not available

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

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

Entity Sequences (FASTA):
Capsid_protein_p24: MGSSHHHHHHSSGLVPRGSH MTSILDIRQGPKEPFRDYVD RFYKTLRAEQASQEVKNAAT ETLLVQNANPDCKTILKALG PAATLEEMMTACQGVGGPGH KARVL
NYAD-13_Peptide_Inhibitor: ITFXDLLXYYGKKK

Data sets:
Data typeCount
13C chemical shifts377
15N chemical shifts94
1H chemical shifts713

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Capsid_protein_p241
2NYAD-13_Peptide_Inhibitor2

Entities:

Entity 1, Capsid_protein_p24 105 residues - Formula weight is not available

1   METGLYSERSERHISHISHISHISHISHIS
2   SERSERGLYLEUVALPROARGGLYSERHIS
3   METTHRSERILELEUASPILEARGGLNGLY
4   PROLYSGLUPROPHEARGASPTYRVALASP
5   ARGPHETYRLYSTHRLEUARGALAGLUGLN
6   ALASERGLNGLUVALLYSASNALAALATHR
7   GLUTHRLEULEUVALGLNASNALAASNPRO
8   ASPCYSLYSTHRILELEULYSALALEUGLY
9   PROALAALATHRLEUGLUGLUMETMETTHR
10   ALACYSGLNGLYVALGLYGLYPROGLYHIS
11   LYSALAARGVALLEU

Entity 2, NYAD-13_Peptide_Inhibitor 14 residues - Formula weight is not available

X=MK8 cis double bond between CE atoms of residue 4 and 8.

1   ILETHRPHEMK8ASPLEULEUMK8TYRTYR
2   GLYLYSLYSLYS

Samples:

sample_1: Capsid protein p24, [U-100% 13C; U-100% 15N], 600 uM; NYAD-13 Peptide Inhibitor 900 uM; DTT 2 mM; ammonium acetate 100 mM; H2O 90%; D2O 10%

sample_2: Capsid protein p24, [U-100% 13C; U-100% 15N], 600 uM; NYAD-13 Peptide Inhibitor 900 uM; DTT 2 mM; ammonium acetate 100 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D f1,f2 filtered 1H-1H NOESYsample_1isotropicsample_conditions_1
2D f2 filtered 1H-1H NOESYsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

ARIA v2.2, Linge, O, . - refinement

CARA v1.5, Keller, Wuthrich - chemical shift assignment, peak picking

TOPSPIN v1.3, Bruker Biospin - processing

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 900 MHz

Related Database Links:

BMRB 15137 16555 17738 19264 25532
PDB
DBJ BAA00992 BAA12988 BAA12996 BAA93785 BAA93786
EMBL CAA82791 CAA82793 CAB85858 CAB85866 CAB87157
GB AAA44201 AAA44306 AAA44652 AAA76686 AAB04036
PIR FOVWLV
PRF 1102247B 1103299C
REF NP_057849 NP_057850 NP_579880
SP P03347 P03348 P03366 P03367 P04585

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts