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 19575

Title: HIV-1 capsid protein in tubular assemblies   PubMed: 24370930

Authors: Bayro, Marvin; Chen, Bo; Yau, Wai-Ming; Tycko, Robert

Citation: Bayro, Marvin; Chen, Bo; Yau, Wai-Ming; Tycko, Robert. "Site-specific structural variations accompanying tubular assembly of the HIV-1 capsid protein."  J. Mol. Biol. 426, 1109-1127 (2014).

Assembly members:
HIV1_CA, polymer, 231 residues, Formula weight is not available

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):
HIV1_CA: 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
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Tubule1

Entities:

Entity 1, Tubule 231 residues - Formula weight is not available

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:

U-CA: HIV1_CA, [U-100% 13C; U-100% 15N], 15 mM; NaCl 1 M

13-CA: HIV1_CA, U-15N, [1,3-13C2]Glycerol, 15 mM; NaCl 1 M

2-CA: HIV1_CA, U-15N; [2-13C]Glycerol, 15 mM; NaCl 1 M

sample_conditions_1: ionic strength: 1 M; pH: 8; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
3D NCACXU-CAsolidsample_conditions_1
3D NCOCXU-CAsolidsample_conditions_1
3D NCACX13-CAsolidsample_conditions_1
3D NCOCX13-CAsolidsample_conditions_1
3D CONCA13-CAsolidsample_conditions_1
3D CONCA2-CAsolidsample_conditions_1
3D NCXCYU-CAsolidsample_conditions_1
3D NCXCY13-CAisotropicsample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

MCASSIGN2, Robert Tycko - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

  • Varian InfinityPlus 600 MHz
  • Bruker Avance III 900 MHz

Related Database Links:

BMRB 17738 19261 19264 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