BMRB Entry 19002

Name: Solution structure of the Core Domain (11-85) of the Murine Norovirus VPg protein.
Published: 2013-03-21

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PDB ID: 2m4g
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19002
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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 structure of the Core Domain (11-85) of the Murine Norovirus VPg protein.

Deposition date:

2013-02-05

Original release date:

2013-03-21

Authors:

Leen, Eoin; Kwok, Rex; Birtley, James; Prater, Sean; Simpson, Pete; Matthews, Steve; Marchant, Jan; Curry, Stephen

Citation:

Citation: Leen, Eoin; Kwok, K. Y Rex; Birtley, James; Simpson, Peter; Subba-Reddy, Chennareddy; Chaudhry, Yasmin; Sosnovtsev, Stanislav; Green, Kim; Prater, Sean; Tong, Michael; Young, Joanna; Chung, Liliane; Marchant, Jan; Roberts, Lisa; Kao, C. Cheng; Matthews, Stephen; Goodfellow, Ian; Curry, Stephen. "Structures of the Compact Helical Core Domains of Feline Calicivirus and Murine Norovirus VPg Proteins." J. Virol. 87, 5318-5330 (2013).
PubMed: 23487472

Assembly members:

Assembly members:
MNV_VPg, polymer, 75 residues, 8876.859 Da.

Natural source:

Natural source: Common Name: Murine norovirus Taxonomy ID: 357231 Superkingdom: Viruses Kingdom: not available Genus/species: Murine Norovirus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pETM11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MNV_VPg: GRPGVFRTRGLTDEEYDEFK KRRESRGGKYSIDDYLADRE REEELLERDEEEAIFGDGFG LKATRRSRKAERAKL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	330
15N chemical shifts	75
1H chemical shifts	507

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MNV_VPg	1

Entities:

Entity 1, MNV_VPg 75 residues - 8876.859 Da.

1

GLY

ARG

PRO

GLY

VAL

PHE

ARG

THR

ARG

GLY

2

LEU

THR

ASP

GLU

TYR

ASP

GLU

PHE

LYS

3

LYS

ARG

GLU

SER

ARG

GLY

LYS

TYR

4

SER

ILE

ASP

TYR

LEU

ALA

ASP

ARG

GLU

5

ARG

GLU

LEU

GLU

ARG

ASP

GLU

6

GLU

ALA

ILE

PHE

GLY

ASP

GLY

PHE

GLY

7

LEU

LYS

ALA

THR

ARG

SER

ARG

LYS

ALA

8

GLU

ARG

ALA

LYS

LEU

Samples:

sample_1: MNV VPg 11-85, [U-98% 13C; U-98% 15N], 590 uM; sodium phosphate 50 mM; Sodium chloride 300 mM; DTT 1 mM; H2O 90%; D2O 10%

sample_2: MNV VPg 11-85, [U-98% 13C; U-98% 15N], 710 uM; sodium chloride 360 mM; sodium azide 0.1 w/v; DTT 1 mM; sodium phosphate pH 6.5 60 mM; D2O 100%

sample_conditions_1: ionic strength: 300 mM; pH: 6.5; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 360 mM; pH: 6.5; pressure: 1 Pa; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D H(C)CH-TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_2
3D (H)CCH-TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_2
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D H(CC)(CO)NH	sample_1	isotropic	sample_conditions_1
3D (H)C(CCO)NH	sample_1	isotropic	sample_conditions_1
3D (HB)CB(CGCD)HD	sample_2	isotropic	sample_conditions_2
3D (HB)CB(CGCDCE)HE	sample_2	isotropic	sample_conditions_2
3D HBHA(CBCACO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

ARIA, Linge, O'Donoghue and Nilges - structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

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

MARS, Zweckstetter et al., 2004 - chemical shift assignment

NMR spectrometers:

Bruker Avance 800 MHz

PDB	2M4G
GB	AAO63098 ABB90153 ABJ98943 ABS29272 ABS29274
REF	YP_720001 YP_724459