BMRB Entry 19261

Title:
HIV capsid dimer structure
Deposition date:
2013-05-23
Original release date:
2013-12-09
Authors:
Deshmukh, Lalit; Schwieters, Charles; Grishaev, Alexander; Clore, G. Marius; Ghirlando, Rodolfo
Citation:

Citation: Deshmukh, Lalit; Schwieters, Charles; Grishaev, Alexander; Ghirlando, Rodolfo; Baber, James; Clore, G. Marius. "Structure and Dynamics of Full-Length HIV-1 Capsid Protein in Solution."  J. Am. Chem. Soc. 135, 16133-16147 (2013).
PubMed: 24066695

Assembly members:

Assembly members:
HIVcapsid, polymer, 231 residues, 24654.443 Da.

Natural source:

Natural source:   Common Name: HIV   Taxonomy ID: 12721   Superkingdom: Viruses   Kingdom: not available   Genus/species: Lentivirus Human immunodeficiency virus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET11a

Data sets:
Data typeCount
13C chemical shifts563
15N chemical shifts178
1H chemical shifts178

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1HIV capsid, 11
2HIV capsid, 21

Entities:

Entity 1, HIV capsid, 1 231 residues - 24654.443 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: HIVcapsid, [U-13C; U-15N; U-2H], 0.5 mM; EDTA 1 mM; sodium chloride 50 mM; DTT 1 mM; sodium phosphate 20 mM; H2O 95%; D2O, [U-100% 2H], 5%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D TROSY-Artsysample_1isotropicsample_conditions_1
2D 1H-15N R1sample_1isotropicsample_conditions_1
2D 1H-15N R1sample_1isotropicsample_conditions_1
2D 1H-15N R1rsample_1isotropicsample_conditions_1
2D 1H-15N R1rsample_1isotropicsample_conditions_1
2D 1H-15N HetNOEsample_1isotropicsample_conditions_1
2D 1H-15N HetNOEsample_1isotropicsample_conditions_1

Software:

X-PLOR NIH v2.32, Schwieters, Kuszewski, Tjandra and Clore - refinement

TOPSPIN v1.3, Bruker Biospin - collection

CCPN-Analysis v2.2.2, (CCPN-Analysis)-Vranken, Boucher, Stevens..Laue. - data analysis

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 500 MHz

Related Database Links:

BMRB 17738 19264 19575 25532
PDB
DBJ BAA00992 BAA12988 BAA12996 BAA93773 BAA93774
EMBL CAA06946 CAA11884 CAA11886 CAA25902 CAA65355
GB AAA44201 AAA44225 AAA44306 AAA44652 AAA44691
PIR FOVWLV
PRF 1102247B 1103299C
REF NP_057849 NP_057850 NP_579880
SP P03347 P03348 P03349 P03366 P03367
AlphaFold P03349 P03348 P03347 P03366 P03367

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks