BMRB Entry 25404

Name: Solution structure of VPg of porcine sapovirus
Published: 2015-04-13

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PDB ID: 2mxd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25404
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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 VPg of porcine sapovirus

Deposition date:

2014-12-24

Original release date:

2015-04-13

Authors:

Kim, Jeong-Sun; Hwang, Hyo-Jeong; Min, Hye Jung; Yun, Hyosuk; Cho, Kyoung-Oh; Pelton, Jeffrey; Wemmer, David; Lee, Chul Won

Citation:

Citation: Hwang, Hyo-Jeong; Min, Hye Jung; Yun, Hyosuk; Pelton, Jeffrey; Wemmer, David; Cho, Kyoung-Oh; Kim, Jeong-Sun; Lee, Chul Won. "Solution structure of the porcine sapovirus VPg core reveals a stable three-helical bundle with a conserved surface patch" Biochem. Biophys. Res. Commun. 459, 610-616 (2015).
PubMed: 25753201

Assembly members:

Assembly members:
entity, polymer, 62 residues, 7382.292 Da.

Natural source:

Natural source: Common Name: PEDV Taxonomy ID: 28295 Superkingdom: Viruses Kingdom: not available Genus/species: Alphacoronavirus Porcine epidemic diarrhea virus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GAMAIALRDDEYDEWQDIIR DWRKEMTVQQFLDLKERALS GASDPDSQRYNAWLELRAKR LS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	277
15N chemical shifts	67
1H chemical shifts	443

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity	1

Entities:

Entity 1, entity 62 residues - 7382.292 Da.

1

GLY

ALA

MET

ALA

ILE

ALA

LEU

ARG

ASP

2

GLU

TYR

ASP

GLU

TRP

GLN

ASP

ILE

ARG

3

ASP

TRP

ARG

LYS

GLU

MET

THR

VAL

GLN

4

PHE

LEU

ASP

LEU

LYS

GLU

ARG

ALA

LEU

SER

5

GLY

ALA

SER

ASP

PRO

ASP

SER

GLN

ARG

TYR

6

ASN

ALA

TRP

LEU

GLU

LEU

ARG

ALA

LYS

ARG

7

LEU

SER

Samples:

sample_1: entity, [U-99% 13C; U-99% 15N], 1 mM; potassium phosphate 10 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 10 mM; pH: 6.2; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	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 HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker DRX 600 MHz

PDB	2MXD
GB	AAF04560 AAR37376 ACP43737 AFX61394 AGW22217
REF	NP_051035
SP	Q9QEJ5
AlphaFold	Q9QEJ5