BMRBj - BMREntryMaster

Found 1 Document (0.349 seconds)

BMRB: 30739

6WA4

Solution NMR structure of the unmyristoylated feline immunodeficiency virus matrix protein

Authors

Brown, J.B., Summers, H.R., Brown, L.A., Marchant, J., Canova, P.N., O'Hern, C.T., Abbott, S.T., Nyaunu, C., Maxwell, S., Johnson, T., Moser, M.B., Carter, H., Ablan, S., Freed, E.O., Summers, M.F.

Assembly

Matrix protein

Entity

1. Matrix protein (polymer), 126 monomers, 13962.80 Da Detail

GNGQGRDWKM AIKRCSNVAV GVGGKSKKFG EGNFRWAIRM ANVSTGREPG DIPETLDQLR LVICDLQERR EKFGSSKEID MAIVTLKVFA VAGLLNMTVS TAAAAENMYS QMGLDTRPHH HHHHHH

Formula weight

13962.8 Da

Source organism

Feline immunodeficiency virus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.7 %, Completeness: 75.4 %, Completeness (bb): 88.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.4 % (1086 of 1441)	66.7 % (497 of 745)	83.9 % (463 of 552)	87.5 % (126 of 144)
Backbone	88.7 % (665 of 750)	83.6 % (219 of 262)	91.0 % (332 of 365)	92.7 % (114 of 123)
Sidechain	65.2 % (524 of 804)	57.6 % (278 of 483)	78.0 % (234 of 300)	57.1 % (12 of 21)
Aromatic	42.3 % (44 of 104)	38.5 % (20 of 52)	44.0 % (22 of 50)	100.0 % (2 of 2)
Methyl	77.8 % (98 of 126)	77.8 % (49 of 63)	77.8 % (49 of 63)

1. entity 1

GNGQGRDWKM AIKRCSNVAV GVGGKSKKFG EGNFRWAIRM ANVSTGREPG DIPETLDQLR LVICDLQERR EKFGSSKEID MAIVTLKVFA VAGLLNMTVS TAAAAENMYS QMGLDTRPHH HHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	10 mM
3	sodium chloride	natural abundance	5 mM
4	glucose	natural abundance	4 g/L
5	ammonium chloride	[U-99% 15N]	1 g/L
6	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-15N]	300 uM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM [U-98% 2H] DTT, 5 mM sodium chloride, 300 uM Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 100% D2O

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	DTT	[U-98% 2H]	10 mM
9	sodium chloride	natural abundance	5 mM
10	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	natural abundance	300 uM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-13C; U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	sodium phosphate	natural abundance	50 mM
12	DTT	natural abundance	10 mM
13	sodium chloride	natural abundance	5 mM
14	glucose	[U-99% 13C]	4 g/L
15	ammonium chloride	[U-99% 15N]	1 g/L
16	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C; U-15N]	300 uM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM [U-98% 2H] DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L ammonium chloride, 300 uM [U-13C] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 100% D2O

#	Name	Isotope labeling	Concentration
17	sodium phosphate	natural abundance	50 mM
18	DTT	[U-98% 2H]	10 mM
19	sodium chloride	natural abundance	5 mM
20	glucose	[U-99% 13C]	4 g/L
21	ammonium chloride	natural abundance	1 g/L
22	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C]	300 uM

Release date

2020-04-06

Citation

Structural and Mechanistic Studies of the Rare Myristoylation Signal of the Feline Immunodeficiency Virus
Brown, J.B., Summers, H.R., Brown, L.A., Marchant, J., Canova, P.N., O'Hern, C.T., Abbott, S.T., Nyaunu, C., Maxwell, S., Johnson, T., Moser, M.B., Carter, H., Ablan, S., Freed, E.O., Summers, M.F.
J. Mol. Biol. (2020), 432, 4076-4091, PubMed 32442659 , DOI 10.1016/j.jmb.2020.05.008 , Abstract

Related entities 1. Matrix protein, : 1 : 3 : 6 entities Detail

Experiments performed 18 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM [U-98% 2H] DTT, 5 mM sodium chloride, 300 uM Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 100% D2O

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	DTT	[U-98% 2H]	10 mM
9	sodium chloride	natural abundance	5 mM
10	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	natural abundance	300 uM

2 2D 1H-1H NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 50 mM sodium phosphate, 10 mM [U-98% 2H] DTT, 5 mM sodium chloride, 300 uM Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 100% D2O

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	DTT	[U-98% 2H]	10 mM
9	sodium chloride	natural abundance	5 mM
10	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	natural abundance	300 uM

3 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	10 mM
3	sodium chloride	natural abundance	5 mM
4	glucose	natural abundance	4 g/L
5	ammonium chloride	[U-99% 15N]	1 g/L
6	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-15N]	300 uM

4 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	10 mM
3	sodium chloride	natural abundance	5 mM
4	glucose	natural abundance	4 g/L
5	ammonium chloride	[U-99% 15N]	1 g/L
6	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-15N]	300 uM

5 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-13C; U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	sodium phosphate	natural abundance	50 mM
12	DTT	natural abundance	10 mM
13	sodium chloride	natural abundance	5 mM
14	glucose	[U-99% 13C]	4 g/L
15	ammonium chloride	[U-99% 15N]	1 g/L
16	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C; U-15N]	300 uM

6 3D HNCO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-13C; U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	sodium phosphate	natural abundance	50 mM
12	DTT	natural abundance	10 mM
13	sodium chloride	natural abundance	5 mM
14	glucose	[U-99% 13C]	4 g/L
15	ammonium chloride	[U-99% 15N]	1 g/L
16	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C; U-15N]	300 uM

7 3D HNCO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-13C; U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	sodium phosphate	natural abundance	50 mM
12	DTT	natural abundance	10 mM
13	sodium chloride	natural abundance	5 mM
14	glucose	[U-99% 13C]	4 g/L
15	ammonium chloride	[U-99% 15N]	1 g/L
16	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C; U-15N]	300 uM

8 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-13C; U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	sodium phosphate	natural abundance	50 mM
12	DTT	natural abundance	10 mM
13	sodium chloride	natural abundance	5 mM
14	glucose	[U-99% 13C]	4 g/L
15	ammonium chloride	[U-99% 15N]	1 g/L
16	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C; U-15N]	300 uM

9 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-13C; U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	sodium phosphate	natural abundance	50 mM
12	DTT	natural abundance	10 mM
13	sodium chloride	natural abundance	5 mM
14	glucose	[U-99% 13C]	4 g/L
15	ammonium chloride	[U-99% 15N]	1 g/L
16	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C; U-15N]	300 uM

10 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-13C; U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	sodium phosphate	natural abundance	50 mM
12	DTT	natural abundance	10 mM
13	sodium chloride	natural abundance	5 mM
14	glucose	[U-99% 13C]	4 g/L
15	ammonium chloride	[U-99% 15N]	1 g/L
16	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C; U-15N]	300 uM

11 2D 1H-15N HSQC

Instrument

Bruker DMX - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	10 mM
3	sodium chloride	natural abundance	5 mM
4	glucose	natural abundance	4 g/L
5	ammonium chloride	[U-99% 15N]	1 g/L
6	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-15N]	300 uM

12 2D 1H-13 HMQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM [U-98% 2H] DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L ammonium chloride, 300 uM [U-13C] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 100% D2O

#	Name	Isotope labeling	Concentration
17	sodium phosphate	natural abundance	50 mM
18	DTT	[U-98% 2H]	10 mM
19	sodium chloride	natural abundance	5 mM
20	glucose	[U-99% 13C]	4 g/L
21	ammonium chloride	natural abundance	1 g/L
22	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C]	300 uM

13 4D HMQC-NOESY-HMQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM [U-98% 2H] DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L ammonium chloride, 300 uM [U-13C] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 100% D2O

#	Name	Isotope labeling	Concentration
17	sodium phosphate	natural abundance	50 mM
18	DTT	[U-98% 2H]	10 mM
19	sodium chloride	natural abundance	5 mM
20	glucose	[U-99% 13C]	4 g/L
21	ammonium chloride	natural abundance	1 g/L
22	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C]	300 uM

14 4D HSQC-NOESY-HMQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-13C; U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	sodium phosphate	natural abundance	50 mM
12	DTT	natural abundance	10 mM
13	sodium chloride	natural abundance	5 mM
14	glucose	[U-99% 13C]	4 g/L
15	ammonium chloride	[U-99% 15N]	1 g/L
16	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C; U-15N]	300 uM

15 3D 1H-15N NOESY

Instrument

Bruker DMX - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	10 mM
3	sodium chloride	natural abundance	5 mM
4	glucose	natural abundance	4 g/L
5	ammonium chloride	[U-99% 15N]	1 g/L
6	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-15N]	300 uM

16 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	10 mM
3	sodium chloride	natural abundance	5 mM
4	glucose	natural abundance	4 g/L
5	ammonium chloride	[U-99% 15N]	1 g/L
6	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-15N]	300 uM

17 3D HN(CA)CO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-13C; U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	sodium phosphate	natural abundance	50 mM
12	DTT	natural abundance	10 mM
13	sodium chloride	natural abundance	5 mM
14	glucose	[U-99% 13C]	4 g/L
15	ammonium chloride	[U-99% 15N]	1 g/L
16	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C; U-15N]	300 uM

18 3D HN(CA)CO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 50 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-13C; U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	sodium phosphate	natural abundance	50 mM
12	DTT	natural abundance	10 mM
13	sodium chloride	natural abundance	5 mM
14	glucose	[U-99% 13C]	4 g/L
15	ammonium chloride	[U-99% 15N]	1 g/L
16	Unmyristoylated Feline Immunodeficiency Virus Matrix Protein	[U-13C; U-15N]	300 uM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30739_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30739_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1207		92.9 (chain: 1, length: 126)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 126, Sequence coverage: 92.9%
- Total number of assignments
  - ¹H chemical shifts: 611
  - ¹³C chemical shifts: 472
  - ¹⁵N chemical shifts: 124
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
57	ASP	CG	178.3422

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	745	501	67.2
¹³C chemical shifts	552	471	85.3
¹⁵N chemical shifts	144	124	86.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	262	229	87.4
¹³C chemical shifts	252	234	92.9
¹⁵N chemical shifts	123	113	91.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	483	272	56.3
¹³C chemical shifts	300	237	79.0
¹⁵N chemical shifts	21	11	52.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	55	79.7
¹³C chemical shifts	69	54	78.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	23	44.2
¹³C chemical shifts	50	21	42.0
¹⁵N chemical shifts	2	2	100.0

Keywords FIV, VIRAL PROTEIN

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Found 1 Document (0.349 seconds)

BMRB: 30739

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Sample #4

Related entities 1. Matrix protein, : 1 : 3 : 6 entities Detail

Experiments performed 18 experiments Detail

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Chemical shift validation 3 contents Detail