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BMRB Entry 18716

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18716
MolProbity Validation Chart

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

Deposition date: 2012-09-14 Original release date: 2013-02-11

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

Download simulated HSQC data in one of the following formats:
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SPARKY: Backbone or all simulated shifts