BMRB Entry 19003

Name: Solution structure of the Core Domain (10-76) of the Feline Calicivirus VPg protein.
Published: 2013-03-21

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PDB ID: 2m4h
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19003
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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 (10-76) of the Feline Calicivirus VPg protein.

Deposition date:

2013-02-05

Original release date:

2013-03-21

Authors:

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

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:
FCV_VPg, polymer, 71 residues, 7906.722 Da.

Natural source:

Natural source: Common Name: Feline calicivirus Taxonomy ID: 11978 Superkingdom: Viruses Kingdom: not available Genus/species: Feline calicivirus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pQE30

Entity Sequences (FASTA):

Entity Sequences (FASTA):
FCV_VPg: IGTYRGRGVALTDDEYDEWR EHNASRKLDLSVEDFLMLRH RAALGADDNDAVKFRSWWNS RTKMANDYEDV

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	307
15N chemical shifts	81
1H chemical shifts	465

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	FCV_VPg_9-76	1

Entities:

Entity 1, FCV_VPg_9-76 71 residues - 7906.722 Da.

1

ILE

GLY

THR

TYR

ARG

GLY

ARG

GLY

VAL

ALA

2

LEU

THR

ASP

GLU

TYR

ASP

GLU

TRP

ARG

3

GLU

HIS

ASN

ALA

SER

ARG

LYS

LEU

ASP

LEU

4

SER

VAL

GLU

ASP

PHE

LEU

MET

LEU

ARG

HIS

5

ARG

ALA

LEU

GLY

ALA

ASP

ASN

ASP

6

ALA

VAL

LYS

PHE

ARG

SER

TRP

ASN

SER

7

ARG

THR

LYS

MET

ALA

ASN

ASP

TYR

GLU

ASP

8

VAL

Samples:

sample_1: FCV VPg 7-76, [U-99% 13C; U-99% 15N], 100 – 200 uM; sodium chloride 300 mM; HEPES pH7 20 mM; sodium azide 1 mM; H2O 90%; D2O 10%

sample_2: FCV VPg 7-76, [U-99% 13C; U-99% 15N], 100 – 200 uM; sodium chloride 300 mM; sodium azide 1 mM; HEPES pH7 20 mM; D2O 100%

sample_3: FCV VPg 7-76, [U-99% 13C; U-99% 15N], 100 – 200 uM; sodium chloride 300 mM; sodium azide 1 mM; HEPES pH7 20 mM; Pf1 phage 15 mg/mL; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 300 mM; pH: 7; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 300 mM; pH: 7; pressure: 1 bar; temperature: 283 K

sample_conditions_3: ionic strength: 300 mM; pH: 7; pressure: 1 Pa; temperature: 280 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
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 HBHA(CBCACO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_3	anisotropic	sample_conditions_3
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1

Software:

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

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

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

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

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

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

NMR spectrometers:

Bruker DRX 500 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