BMRB Entry 16889

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16889
MolProbity Validation Chart

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Title:
Solution structure of HIV-2 myrMA bound to di-C4-PI(4,5)P2
Deposition date:
2010-04-21
Original release date:
2012-08-02
Authors:
Saad, Jamil; Ablan, Sherimay; Ghanam, Ruba; Kim, Andrew; Andrews, Kalola; Nagashima, Kunio; Freed, Eric; Summers, Michael
Citation:

Citation: Saad, Jamil; Ablan, Sherimay; Ghanam, Ruba; Kim, Andrew; Andrews, Kalola; Nagashima, Kunio; Soheilian, Ferri; Freed, Eric; Summers, Michael. "Structure of the myristylated human immunodeficiency virus type 2 matrix protein and the role of phosphatidylinositol-(4,5)-bisphosphate in membrane targeting."  J. Mol. Biol. 382, 434-447 (2008).
PubMed: 18657545

Assembly members:

Assembly members:
HIV-2, polymer, 135 residues, 14899.383 Da.
PBU, non-polymer, 634.354 Da.

Natural source:

Natural source:   Common Name: Human immunodeficiency virus 2   Taxonomy ID: 11709   Superkingdom: virus   Kingdom: not available   Genus/species: Lentivirus HIV2

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET 11 and 19

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HIV-2: XGARNSVLRGKKADELERIR LRPGGKKKYRLKHIVWAANK LDRFGLAESLLESKEGCQKI LTVLDPMVPTGSENLKSLFN TVCVIWCIHAEEKVKDTEGA KQIVRRHLVAETGTAEKMPS TSRPTAPSSEKGGNY

Data sets:
Data typeCount
13C chemical shifts402
15N chemical shifts128
1H chemical shifts789

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1HIV-2 myrMA bound to di-C4-PI(4,5)P21
2PBU2

Entities:

Entity 1, HIV-2 myrMA bound to di-C4-PI(4,5)P2 135 residues - 14899.383 Da.

1   MYRGLYALAARGASNSERVALLEUARGGLY
2   LYSLYSALAASPGLULEUGLUARGILEARG
3   LEUARGPROGLYGLYLYSLYSLYSTYRARG
4   LEULYSHISILEVALTRPALAALAASNLYS
5   LEUASPARGPHEGLYLEUALAGLUSERLEU
6   LEUGLUSERLYSGLUGLYCYSGLNLYSILE
7   LEUTHRVALLEUASPPROMETVALPROTHR
8   GLYSERGLUASNLEULYSSERLEUPHEASN
9   THRVALCYSVALILETRPCYSILEHISALA
10   GLUGLULYSVALLYSASPTHRGLUGLYALA
11   LYSGLNILEVALARGARGHISLEUVALALA
12   GLUTHRGLYTHRALAGLULYSMETPROSER
13   THRSERARGPROTHRALAPROSERSERGLU
14   LYSGLYGLYASNTYR

Entity 2, PBU - C17 H33 O19 P3 - 634.354 Da.

1   PBU

Samples:

sample_1: HIV-2 myristoylated matrix protein, [U-15N], 0.8 mM; potassium phosphate 20 mM; DTT 10 mM; Glutamate 50 mM; Aspartate 50 mM; sodium chloride 100 mM; H2O 90%; D2O 10%

sample_2: HIV-2 myristoylated matrix protein 0.8 mM; potassium phosphate 20 mM; DTT 10 mM; Glutamate 50 mM; Aspartate 50 mM; sodium chloride 100 mM; D2O 100%

sample_3: HIV-2 myristoylated matrix protein, [U-13C; U-15N], 0.8 mM; potassium phosphate 20 mM; DTT 10 mM; Glutamate 50 mM; Aspartate 50 mM; sodium chloride 100 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.1 M; pH: 6.3; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
3D HN(CO)CAsample_3isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - refinement

NMR spectrometers:

  • Bruker DRX 800 MHz
  • Bruker DMX 600 MHz

Related Database Links:

BMRB 16887 16888
PDB
EMBL CAA28909
GB AAB00763
PRF 1306388A
SP P04584 P04590
AlphaFold P04584 P04590

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