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 18716

Title: Structure of HIV-1 myr(-) matrix protein in complex with 1,2-dioctanoyl-sn-phosphatidyl-L-serine

Authors: Vlach, Jiri; Saad, Jamil

Citation: Vlach, Jiri; Saad, Jamil. "Model for the interaction between HIV-1 Gag and plasma membrane"  Proc. Natl. Acad. Sci. U.S.A. ., .-..

Assembly members:
MA, polymer, 131 residues, 14734.753 Da.
O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine, non-polymer, 511.543 Da.

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

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

Entity Sequences (FASTA):
MA: GARASVLSGGELDKWEKIRL RPGGKKQYKLKHIVWASREL ERFAVNPGLLETSEGCRQIL GQLQPSLQTGSEELRSLYNT IAVLYCVHQRIDVKDTKEAL DKIEEEQNKSKKKAQQAAAD TGNNSQVSQNY

Data sets:
Data typeCount
13C chemical shifts434
15N chemical shifts131
1H chemical shifts887

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1HIV-1 myr(-) matrix protein1
28SP2

Entities:

Entity 1, HIV-1 myr(-) matrix protein 131 residues - 14734.753 Da.

1   GLYALAARGALASERVALLEUSERGLYGLY
2   GLULEUASPLYSTRPGLULYSILEARGLEU
3   ARGPROGLYGLYLYSLYSGLNTYRLYSLEU
4   LYSHISILEVALTRPALASERARGGLULEU
5   GLUARGPHEALAVALASNPROGLYLEULEU
6   GLUTHRSERGLUGLYCYSARGGLNILELEU
7   GLYGLNLEUGLNPROSERLEUGLNTHRGLY
8   SERGLUGLULEUARGSERLEUTYRASNTHR
9   ILEALAVALLEUTYRCYSVALHISGLNARG
10   ILEASPVALLYSASPTHRLYSGLUALALEU
11   ASPLYSILEGLUGLUGLUGLNASNLYSSER
12   LYSLYSLYSALAGLNGLNALAALAALAASP
13   THRGLYASNASNSERGLNVALSERGLNASN
14   TYR

Entity 2, 8SP - C22 H42 N O10 P - 511.543 Da.

1   8SP

Samples:

sample_1: MA, [U-95% 13C], 0.4 mM; 1,2-dioctanoyl-sn-glycero-3-phospho-L-serine, sodium salt0.8 – 1.0 mM; sodium phosphate 50 mM; DTT 2 mM; H2O 90%; D2O 10%

sample_2: MA, [U-95% 13C; U-95% 15N], 0.4 – 1.0 mM; 1,2-dioctanoyl-sn-glycero-3-phospho-L-serine, sodium salt0.8 – 1.0 mM; sodium phosphate 50 mM; DTT 2 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 50 mM; pH: 5.5; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
3D 13C-edited/13C-filtered NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1

Software:

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

TOPSPIN, Bruker Biospin - collection

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

CCPN_Analysis, CCPN - data analysis

NMR spectrometers:

  • Bruker Avance II 700 MHz

Related Database Links:

EMBL P12493 CBI61180 CBI61181 CBI61182 CBI61183 CBI61184
BMRB 15114 15116 18715
PDB
DBJ BAF34641 BAG48474
GB AAA44987 AAB00898 AAB60571 AAC28445 AAC29216
SP P12493 P12497