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 25532

Title: Conformation and dynamics of the Gag polyprotein of the human immunodeficiency virus 1 studied by NMR spectroscopy.   PubMed: 25713345

Authors: Deshmukh, Lalit; Clore, Marius

Citation: Deshmukh, Lalit; Ghirlando, Rodolfo; Clore, Marius. "Conformation and dynamics of the Gag polyprotein of the human immunodeficiency virus 1 studied by NMR spectroscopy."  P. Natl. Acad. Sci. U.S.A. 112, 3374-3379 (2015).

Assembly members:
Gag, polymer, 432 residues, Formula weight is not available

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

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

Entity Sequences (FASTA):
Gag: MGARASVLSGGELDRWEKIR LRPGGKKKYKLKHIVWASRE LERFAVNPGLLETSEGCRQI LGQLQPSLQTGSEELRSLYN TVATLYCVHQRIEIKDTKEA LDKIEEEQNKSKKKAQQAAA DTGHSNQVSQNYPIVQNIQG QMVHQAISPRTLNAWVKVVE EKAFSPEVIPMFSALSEGAT PQDLNTMLNTVGGHQAAMQM LKETINEEAAEWDRVHPVHA GPIAPGQMREPRGSDIAGTT STLQEQIGWMTNNPPIPVGE IYKRWIILGLNKIVRMYSPT SILDIRQGPKEPFRDYVDRF YKTLRAEQASQEVKNWMTET LLVQNANPDCKTILKALGPA ATLEEMMTACQGVGGPGHKA RVLAEAMSQVTNSATIMMQR GNFRNQRKIVKCFNCGKEGH TARNCRAPRKKGCWKCGKEG HQMKDCTERQAN

Data sets:
Data typeCount
13C chemical shifts1013
15N chemical shifts326
1H chemical shifts326

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Gag1

Entities:

Entity 1, Gag 432 residues - Formula weight is not available

1   METGLYALAARGALASERVALLEUSERGLY
2   GLYGLULEUASPARGTRPGLULYSILEARG
3   LEUARGPROGLYGLYLYSLYSLYSTYRLYS
4   LEULYSHISILEVALTRPALASERARGGLU
5   LEUGLUARGPHEALAVALASNPROGLYLEU
6   LEUGLUTHRSERGLUGLYCYSARGGLNILE
7   LEUGLYGLNLEUGLNPROSERLEUGLNTHR
8   GLYSERGLUGLULEUARGSERLEUTYRASN
9   THRVALALATHRLEUTYRCYSVALHISGLN
10   ARGILEGLUILELYSASPTHRLYSGLUALA
11   LEUASPLYSILEGLUGLUGLUGLNASNLYS
12   SERLYSLYSLYSALAGLNGLNALAALAALA
13   ASPTHRGLYHISSERASNGLNVALSERGLN
14   ASNTYRPROILEVALGLNASNILEGLNGLY
15   GLNMETVALHISGLNALAILESERPROARG
16   THRLEUASNALATRPVALLYSVALVALGLU
17   GLULYSALAPHESERPROGLUVALILEPRO
18   METPHESERALALEUSERGLUGLYALATHR
19   PROGLNASPLEUASNTHRMETLEUASNTHR
20   VALGLYGLYHISGLNALAALAMETGLNMET
21   LEULYSGLUTHRILEASNGLUGLUALAALA
22   GLUTRPASPARGVALHISPROVALHISALA
23   GLYPROILEALAPROGLYGLNMETARGGLU
24   PROARGGLYSERASPILEALAGLYTHRTHR
25   SERTHRLEUGLNGLUGLNILEGLYTRPMET
26   THRASNASNPROPROILEPROVALGLYGLU
27   ILETYRLYSARGTRPILEILELEUGLYLEU
28   ASNLYSILEVALARGMETTYRSERPROTHR
29   SERILELEUASPILEARGGLNGLYPROLYS
30   GLUPROPHEARGASPTYRVALASPARGPHE
31   TYRLYSTHRLEUARGALAGLUGLNALASER
32   GLNGLUVALLYSASNTRPMETTHRGLUTHR
33   LEULEUVALGLNASNALAASNPROASPCYS
34   LYSTHRILELEULYSALALEUGLYPROALA
35   ALATHRLEUGLUGLUMETMETTHRALACYS
36   GLNGLYVALGLYGLYPROGLYHISLYSALA
37   ARGVALLEUALAGLUALAMETSERGLNVAL
38   THRASNSERALATHRILEMETMETGLNARG
39   GLYASNPHEARGASNGLNARGLYSILEVAL
40   LYSCYSPHEASNCYSGLYLYSGLUGLYHIS
41   THRALAARGASNCYSARGALAPROARGLYS
42   LYSGLYCYSTRPLYSCYSGLYLYSGLUGLY
43   HISGLNMETLYSASPCYSTHRGLUARGGLN
44   ALAASN

Samples:

sample_1: Gag, [U-13C; U-15N; U-2H], 0.3 – 0.4 mM; D2O, [U-2H], 7%; sodium phosphate 20 mM; sodium chloride 300 mM; TCEP 1 mM; zinc chloride 0.1 mM; H2O 93%

sample_conditions_1: ionic strength: 310 mM; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1

Software:

Analysis v2.2.2, CCPN - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 500 MHz

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