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Found 1 Document (0.349 seconds)

BMRB: 30738

6WA3

Solution NMR structure of the myristoylated 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., Nyaunu, C., Maxwell, S., Johnson, T., Moser, M., Ablan, S.D., Carter, H., Freed, E.O., Summers, M.F.

Assembly

Matrix protein

Entity

1. Matrix protein, entity 1 (polymer), 125 monomers, 13898.87 Da Detail

XGNGQGRDWK MAIKRCSNVA VGVGGKSKKF GEGNFRWAIR MANVSTGREP GDIPETLDQL RLVICDLQER REKFGSSKEI DMAIVTLKVF AVAGLLNMTV STAAAAENMY SQMGLDTRPH HHHHH

2. Matrix protein, entity MYR (non-polymer), 228.371 Da

Total weight

14127.241 Da

Max. entity weight

13898.87 Da

Source organism

Feline immunodeficiency virus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.4 %, Completeness: 72.9 %, Completeness (bb): 84.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	72.9 % (1033 of 1417)	65.6 % (481 of 733)	81.0 % (439 of 542)	79.6 % (113 of 142)
Backbone	84.7 % (625 of 738)	79.8 % (206 of 258)	88.3 % (317 of 359)	84.3 % (102 of 121)
Sidechain	64.1 % (506 of 790)	57.9 % (275 of 475)	74.8 % (220 of 294)	52.4 % (11 of 21)
Aromatic	45.8 % (44 of 96)	47.9 % (23 of 48)	41.3 % (19 of 46)	100.0 % (2 of 2)
Methyl	79.4 % (100 of 126)	77.8 % (49 of 63)	81.0 % (51 of 63)

1. entity 1

XGNGQGRDWK MAIKRCSNVA VGVGGKSKKF GEGNFRWAIR MANVSTGREP GDIPETLDQL RLVICDLQER REKFGSSKEI DMAIVTLKVF AVAGLLNMTV STAAAAENMY SQMGLDTRPH HHHHH

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] Feline Immunodeficiency Virus Myristoylated 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	Feline Immunodeficiency Virus Myristoylated 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, 4 g/L [U-99% 13C] glucose, 1 g/L ammonium chloride, 300 uM [U-13C] Feline Immunodeficiency Virus Myristoylated 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	glucose	[U-99% 13C]	4 g/L
11	ammonium chloride	natural abundance	1 g/L
12	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-13C]	300 uM

Sample #3

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, 50 mg/L Myristoyl coenzyme A, 300 uM [U-13C] Feline Immunodeficiency Virus Myristoylated Matrix Protein, 100% D2O

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	DTT	[U-98% 2H]	10 mM
15	sodium chloride	natural abundance	5 mM
16	glucose	[U-99% 13C]	4 g/L
17	ammonium chloride	natural abundance	1 g/L
18	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-13C]	300 uM
19	Myristoyl coenzyme A	natural abundance	50 mg/L

Sample #4

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] Feline Immunodeficiency Virus Myristoylated Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
20	sodium phosphate	natural abundance	50 mM
21	DTT	natural abundance	10 mM
22	sodium chloride	natural abundance	5 mM
23	glucose	[U-99% 13C]	4 g/L
24	ammonium chloride	[U-99% 15N]	1 g/L
25	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-13C; U-15N]	300 uM

Sample #5

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 glucose, 1 g/L ammonium chloride, 300 uM Feline Immunodeficiency Virus Myristoylated Matrix Protein, 100% D2O

#	Name	Isotope labeling	Concentration
26	sodium phosphate	natural abundance	50 mM
27	DTT	[U-98% 2H]	10 mM
28	sodium chloride	natural abundance	5 mM
29	glucose	natural abundance	4 g/L
30	ammonium chloride	natural abundance	1 g/L
31	Feline Immunodeficiency Virus Myristoylated Matrix Protein	natural abundance	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., Nyaunu, C., Maxwell, S., Johnson, T., Moser, M., Ablan, S.D., Carter, H., 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, entity 1, : 1 : 3 : 6 entities Detail

Experiments performed 11 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, 4 g/L glucose, 1 g/L ammonium chloride, 300 uM Feline Immunodeficiency Virus Myristoylated Matrix Protein, 100% D2O

#	Name	Isotope labeling	Concentration
26	sodium phosphate	natural abundance	50 mM
27	DTT	[U-98% 2H]	10 mM
28	sodium chloride	natural abundance	5 mM
29	glucose	natural abundance	4 g/L
30	ammonium chloride	natural abundance	1 g/L
31	Feline Immunodeficiency Virus Myristoylated Matrix Protein	natural abundance	300 uM

2 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] Feline Immunodeficiency Virus Myristoylated 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	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-15N]	300 uM

3 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] Feline Immunodeficiency Virus Myristoylated Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
20	sodium phosphate	natural abundance	50 mM
21	DTT	natural abundance	10 mM
22	sodium chloride	natural abundance	5 mM
23	glucose	[U-99% 13C]	4 g/L
24	ammonium chloride	[U-99% 15N]	1 g/L
25	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-13C; U-15N]	300 uM

4 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] Feline Immunodeficiency Virus Myristoylated Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
20	sodium phosphate	natural abundance	50 mM
21	DTT	natural abundance	10 mM
22	sodium chloride	natural abundance	5 mM
23	glucose	[U-99% 13C]	4 g/L
24	ammonium chloride	[U-99% 15N]	1 g/L
25	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-13C; U-15N]	300 uM

5 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] Feline Immunodeficiency Virus Myristoylated Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
20	sodium phosphate	natural abundance	50 mM
21	DTT	natural abundance	10 mM
22	sodium chloride	natural abundance	5 mM
23	glucose	[U-99% 13C]	4 g/L
24	ammonium chloride	[U-99% 15N]	1 g/L
25	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-13C; U-15N]	300 uM

6 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] Feline Immunodeficiency Virus Myristoylated Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
20	sodium phosphate	natural abundance	50 mM
21	DTT	natural abundance	10 mM
22	sodium chloride	natural abundance	5 mM
23	glucose	[U-99% 13C]	4 g/L
24	ammonium chloride	[U-99% 15N]	1 g/L
25	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-13C; U-15N]	300 uM

7 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	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-15N]	300 uM

8 2D 1H-13C 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, 50 mg/L Myristoyl coenzyme A, 300 uM [U-13C] Feline Immunodeficiency Virus Myristoylated Matrix Protein, 100% D2O

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	DTT	[U-98% 2H]	10 mM
15	sodium chloride	natural abundance	5 mM
16	glucose	[U-99% 13C]	4 g/L
17	ammonium chloride	natural abundance	1 g/L
18	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-13C]	300 uM
19	Myristoyl coenzyme A	natural abundance	50 mg/L

9 2D 1H-13C 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] Feline Immunodeficiency Virus Myristoylated 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	glucose	[U-99% 13C]	4 g/L
11	ammonium chloride	natural abundance	1 g/L
12	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-13C]	300 uM

10 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] Feline Immunodeficiency Virus Myristoylated 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	glucose	[U-99% 13C]	4 g/L
11	ammonium chloride	natural abundance	1 g/L
12	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-13C]	300 uM

11 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] Feline Immunodeficiency Virus Myristoylated Matrix Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
20	sodium phosphate	natural abundance	50 mM
21	DTT	natural abundance	10 mM
22	sodium chloride	natural abundance	5 mM
23	glucose	[U-99% 13C]	4 g/L
24	ammonium chloride	[U-99% 15N]	1 g/L
25	Feline Immunodeficiency Virus Myristoylated Matrix Protein	[U-13C; U-15N]	300 uM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30738_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: bmr30738_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1165		91.2 (chain: 1, length: 125)
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: 125, Sequence coverage: 91.2%
- Total number of assignments
  - ¹H chemical shifts: 602
  - ¹³C chemical shifts: 449
  - ¹⁵N chemical shifts: 114
- 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)
34	ASN	CG	172.8467
108	ASN	CG	172.8956
112	GLN	CD	177.2162

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	758	486	64.1
¹³C chemical shifts	556	446	80.2
¹⁵N chemical shifts	142	114	80.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	260	218	83.8
¹³C chemical shifts	254	225	88.6
¹⁵N chemical shifts	121	103	85.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	498	268	53.8
¹³C chemical shifts	302	221	73.2
¹⁵N chemical shifts	21	11	52.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	58	82.9
¹³C chemical shifts	70	56	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	23	47.9
¹³C chemical shifts	46	19	41.3
¹⁵N chemical shifts	2	2	100.0

Keywords FIV, VIRAL PROTEIN

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Found 1 Document (0.349 seconds)

BMRB: 30738

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

Experiments performed 11 experiments Detail

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Chemical shift validation 4 contents Detail