BMRB Entry 30738

Name: Solution NMR structure of the myristoylated feline immunodeficiency virus matrix protein
Published: 2020-07-20

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PDB ID: 6wa3
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30738
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR structure of the myristoylated feline immunodeficiency virus matrix protein

Deposition date:

2020-03-24

Original release date:

2020-07-20

Authors:

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

Citation:

Citation: Brown, J.; Summers, H.; Brown, L.; Marchant, J.; Canova, P.; O'Hern, C.; Abbott, S.; Nyaunu, C.; Maxwell, S.; Johnson, T.; Moser, M.; Ablan, S.; Carter, H.; Freed, E.; Summers, M.. "Structural and Mechanistic Studies of the Rare Myristoylation Signal of the Feline Immunodeficiency Virus" J. Mol. Biol. 432, 4076-4091 (2020).
PubMed: 32442659

Assembly members:

Assembly members:
entity_1, polymer, 125 residues, 13922.065 Da.
entity_MYR, non-polymer, 228.371 Da.

Natural source:

Natural source: Common Name: FIV Taxonomy ID: 11673 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus FIV

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XGNGQGRDWKMAIKRCSNVA VGVGGKSKKFGEGNFRWAIR MANVSTGREPGDIPETLDQL RLVICDLQERREKFGSSKEI DMAIVTLKVFAVAGLLNMTV STAAAAENMYSQMGLDTRPH HHHHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	449
15N chemical shifts	114
1H chemical shifts	602

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 125 residues - 13922.065 Da.

1

MYR

GLY

ASN

GLY

GLN

GLY

ARG

ASP

TRP

LYS

2

MET

ALA

ILE

LYS

ARG

CYS

SER

ASN

VAL

ALA

3

VAL

GLY

VAL

GLY

LYS

SER

LYS

PHE

4

GLY

GLU

GLY

ASN

PHE

ARG

TRP

ALA

ILE

ARG

5

MET

ALA

ASN

VAL

SER

THR

GLY

ARG

GLU

PRO

6

GLY

ASP

ILE

PRO

GLU

THR

LEU

ASP

GLN

LEU

7

ARG

LEU

VAL

ILE

CYS

ASP

LEU

GLN

GLU

ARG

8

ARG

GLU

LYS

PHE

GLY

SER

LYS

GLU

ILE

9

ASP

MET

ALA

ILE

VAL

THR

LEU

LYS

VAL

PHE

10

ALA

VAL

ALA

GLY

LEU

ASN

MET

THR

VAL

11

SER

THR

ALA

GLU

ASN

MET

TYR

12

SER

GLN

MET

GLY

LEU

ASP

THR

ARG

PRO

HIS

13

HIS

Entity 2, entity_2 - C14 H28 O2 - 228.371 Da.

1

MYR

Samples:

sample_1: sodium phosphate 50 mM; DTT 10 mM; sodium chloride 5 mM; glucose 4 g/L; ammonium chloride, [U-99% 15N], 1 g/L; Feline Immunodeficiency Virus Myristoylated Matrix Protein, [U-15N], 300 uM

sample_2: sodium phosphate 50 mM; DTT, [U-98% 2H], 10 mM; sodium chloride 5 mM; glucose, [U-99% 13C], 4 g/L; ammonium chloride 1 g/L; Feline Immunodeficiency Virus Myristoylated Matrix Protein, [U-13C], 300 uM

sample_3: sodium phosphate 50 mM; DTT, [U-98% 2H], 10 mM; sodium chloride 5 mM; glucose, [U-99% 13C], 4 g/L; ammonium chloride 1 g/L; Feline Immunodeficiency Virus Myristoylated Matrix Protein, [U-13C], 300 uM; Myristoyl coenzyme A 50 mg/L

sample_4: sodium phosphate 50 mM; DTT 10 mM; sodium chloride 5 mM; glucose, [U-99% 13C], 4 g/L; ammonium chloride, [U-99% 15N], 1 g/L; Feline Immunodeficiency Virus Myristoylated Matrix Protein, [U-13C; U-15N], 300 uM

sample_5: sodium phosphate 50 mM; DTT, [U-98% 2H], 10 mM; sodium chloride 5 mM; glucose 4 g/L; ammonium chloride 1 g/L; Feline Immunodeficiency Virus Myristoylated Matrix Protein 300 uM

sample_conditions_1: ionic strength: 5 mM; pH: 8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 5 mM; pH: 8 pD; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_5	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_4	isotropic	sample_conditions_1
3D HNCACB	sample_4	isotropic	sample_conditions_1
3D HNCO	sample_4	isotropic	sample_conditions_1
3D HN(CA)CO	sample_4	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_3	isotropic	sample_conditions_2
2D 1H-13C HMQC	sample_2	isotropic	sample_conditions_2
4D HMQC-NOESY-HMQC	sample_2	isotropic	sample_conditions_2
4D HSQC-NOESY-HMQC	sample_4	isotropic	sample_conditions_1

Software:

NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

NMRFx, Johnson, One Moon Scientific - processing

CYANA, Guntert, Mumenthaler and Wuthrich - refinement, structure calculation

TopSpin, Bruker Biospin - collection

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

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

NMR spectrometers:

Bruker DMX 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks