BMRB Entry 27506

Name: Chemical shift assignment of the viral protein genome-linked (VPg) from Potato virus Y
Published: 2018-10-03

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PDB ID: 6nfw
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR27506
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:

Chemical shift assignment of the viral protein genome-linked (VPg) from Potato virus Y

Deposition date:

2018-06-05

Original release date:

2018-10-03

Authors:

Coutinho de Oliveira, Luciana; Volpon, Laurent; Osborne, Michael; Borden, Katherine

Citation:

Citation: Coutinho de Oliveira, Luciana; Volpon, Laurent; Osborne, Michael; Borden, Katherine. "Chemical shift assignment of the viral protein genome-linked (VPg) from potato virus Y" Biomol. NMR Assignments 13, 9-13 (2019).
PubMed: 30242622

Assembly members:

Assembly members:
VPg_from_potato_virus_Y, polymer, 153 residues, Formula weight is not available

Natural source:

Natural source: Common Name: potato virus Y Taxonomy ID: 12216 Superkingdom: Viruses Kingdom: not available Genus/species: Potyvirus not available

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VPg_from_potato_virus_Y: GSSAYRKKGKGKGTTVGMGK SSRRFINMYGFDPTEYSFIQ FVDPLTGAQIEENVYADIRD IQERFSEVRKKMVENDDIEM QALGSNTTIHAYFRKDWSDK ALKIDLMPHNPLKVCDKTNG IAKFPERELELRQTGPAVEV DVKDIPAQEVEHE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	481
15N chemical shifts	123
1H chemical shifts	703

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	VPg(-37)	1

Entities:

Entity 1, VPg(-37) 153 residues - Formula weight is not available

The first 2 residues (GS) come from the tag.

1

GLY

SER

ALA

TYR

ARG

LYS

GLY

LYS

2

GLY

LYS

GLY

THR

VAL

GLY

MET

GLY

LYS

3

SER

ARG

PHE

ILE

ASN

MET

TYR

GLY

4

PHE

ASP

PRO

THR

GLU

TYR

SER

PHE

ILE

GLN

5

PHE

VAL

ASP

PRO

LEU

THR

GLY

ALA

GLN

ILE

6

GLU

ASN

VAL

TYR

ALA

ASP

ILE

ARG

ASP

7

ILE

GLN

GLU

ARG

PHE

SER

GLU

VAL

ARG

LYS

8

LYS

MET

VAL

GLU

ASN

ASP

ILE

GLU

MET

9

GLN

ALA

LEU

GLY

SER

ASN

THR

ILE

HIS

10

ALA

TYR

PHE

ARG

LYS

ASP

TRP

SER

ASP

LYS

11

ALA

LEU

LYS

ILE

ASP

LEU

MET

PRO

HIS

ASN

12

PRO

LEU

LYS

VAL

CYS

ASP

LYS

THR

ASN

GLY

13

ILE

ALA

LYS

PHE

PRO

GLU

ARG

GLU

LEU

GLU

14

LEU

ARG

GLN

THR

GLY

PRO

ALA

VAL

GLU

VAL

15

ASP

VAL

LYS

ASP

ILE

PRO

ALA

GLN

GLU

VAL

16

GLU

HIS

GLU

Samples:

VPg(-37)-15N13C-H2O: VPg from potato virus Y, [U-100% 13C; U-100% 15N], 400 uM; sodium phosphate 50 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.02 % v/v

VPg(-37)-2H15N13C-H2O: VPg from potato virus Y, [U-13C; U-15N; U-2H], 400 uM; sodium phosphate 50 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.02 % v/v

VPg(-37)-2H15N13C-D2O: VPg from potato virus Y, [U-13C; U-15N; U-2H], 400 uM; sodium phosphate 50 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.02 % v/v

VPg(-37)-15N13C-D2O: VPg from potato virus Y, [U-100% 13C; U-100% 15N], 400 uM; sodium phosphate 50 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.02 % v/v

sample_condition: pH: 7.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	VPg(-37)-15N13C-H2O	isotropic	sample_condition
2D 1H-15N HSQC	VPg(-37)-2H15N13C-H2O	isotropic	sample_condition
2D 1H-15N HSQC	VPg(-37)-2H15N13C-H2O	isotropic	sample_condition
2D 1H-13C HSQC aliphatic	VPg(-37)-15N13C-D2O	isotropic	sample_condition
2D 1H-13C HSQC aromatic	VPg(-37)-15N13C-D2O	isotropic	sample_condition
3D HNCA	VPg(-37)-15N13C-H2O	isotropic	sample_condition
3D HN(CO)CA	VPg(-37)-15N13C-H2O	isotropic	sample_condition
3D HNCACB	VPg(-37)-15N13C-H2O	isotropic	sample_condition
3D CBCA(CO)NH	VPg(-37)-15N13C-H2O	isotropic	sample_condition
3D HNCO	VPg(-37)-15N13C-H2O	isotropic	sample_condition
3D HN(CA)CO	VPg(-37)-15N13C-H2O	isotropic	sample_condition
3D HNCACB	VPg(-37)-2H15N13C-H2O	isotropic	sample_condition
3D CBCA(CO)NH	VPg(-37)-2H15N13C-H2O	isotropic	sample_condition
3D HNCO	VPg(-37)-2H15N13C-H2O	isotropic	sample_condition
3D HN(CA)CO	VPg(-37)-2H15N13C-H2O	isotropic	sample_condition
3D HCCH-TOCSY	VPg(-37)-2H15N13C-D2O	isotropic	sample_condition
3D H(CCO)NH	VPg(-37)-15N13C-H2O	isotropic	sample_condition
3D C(CO)NH	VPg(-37)-2H15N13C-H2O	isotropic	sample_condition
3D 1H-15N NOESY	VPg(-37)-15N13C-H2O	isotropic	sample_condition
3D 1H-13C NOESY aromatic	VPg(-37)-2H15N13C-D2O	isotropic	sample_condition
3D (H)N(COCA)NH	VPg(-37)-2H15N13C-H2O	isotropic	sample_condition

Software:

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

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

TOPSPIN, Bruker Biospin - collection

SPARKY, Goddard - data analysis

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

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