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BMRB: 18716

2LYB

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

Authors

Vlach, J., Saad, J.

Assembly

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

Entity

1. MA (polymer, Thiol state: all free), 131 monomers, 14711.42 Da Detail

GARASVLSGG ELDKWEKIRL RPGGKKQYKL KHIVWASREL ERFAVNPGLL ETSEGCRQIL GQLQPSLQTG SEELRSLYNT IAVLYCVHQR IDVKDTKEAL DKIEEEQNKS KKKAQQAAAD TGNNSQVSQN Y

2. O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine (non-polymer), 511.543 Da

Total weight

15222.963 Da

Max. entity weight

14711.42 Da

Source organism

Human immunodeficiency virus 1

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.6 %, Completeness (bb): 84.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.6 % (1321 of 1543)	91.0 % (742 of 815)	77.1 % (448 of 581)	89.1 % (131 of 147)
Backbone	84.1 % (656 of 780)	97.8 % (263 of 269)	69.2 % (265 of 383)	100.0 % (128 of 128)
Sidechain	88.7 % (784 of 884)	87.7 % (479 of 546)	94.7 % (302 of 319)	15.8 % (3 of 19)
Aromatic	85.1 % (63 of 74)	86.5 % (32 of 37)	82.9 % (29 of 35)	100.0 % (2 of 2)
Methyl	95.7 % (132 of 138)	94.2 % (65 of 69)	97.1 % (67 of 69)

1. MA

GARASVLSGG ELDKWEKIRL RPGGKKQYKL KHIVWASREL ERFAVNPGLL ETSEGCRQIL GQLQPSLQTG SEELRSLYNT IAVLYCVHQR IDVKDTKEAL DKIEEEQNKS KKKAQQAAAD TGNNSQVSQN Y

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	MA	[U-95% 13C]	0.4 mM
2	1,2-dioctanoyl-sn-glycero-3-phospho-L-serine, sodium salt	natural abundance	0.8 ~ 1.0 mM
3	sodium phosphate	natural abundance	50 mM
4	DTT	natural abundance	2 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.5

#	Name	Isotope labeling	Concentration
7	MA	[U-95% 13C; U-95% 15N]	0.4 ~ 1.0 mM
8	1,2-dioctanoyl-sn-glycero-3-phospho-L-serine, sodium salt	natural abundance	0.8 ~ 1.0 mM
9	sodium phosphate	natural abundance	50 mM
10	DTT	natural abundance	2 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.24 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.24 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LYB, Strand ID: A Detail

Release date

2013-02-10

Citation

Model for the interaction between HIV-1 Gag and plasma membrane
Vlach, J., Saad, J.
Proc. Natl. Acad. Sci. U.S.A.

Related entities 1. MA, : 1 : 14 : 2 : 12 : 91 entities Detail

Interaction partners 1. MA, : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 11 experiments Detail

1 3D 13C-edited/13C-filtered NOESY