BMRB Entry 52218

Name: NMR assignments of capsid protein protrusion domain of Dragon grouper nervous necrosis virus at pH 5
Published: 2024-08-05

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52218

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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:

NMR assignments of capsid protein protrusion domain of Dragon grouper nervous necrosis virus at pH 5

Deposition date:

2023-11-29

Original release date:

2024-08-05

Authors:

Sterbova, Petra; Lou, Yuan-Chao; Tzou, Der-Lii; Chang, Wei-Hau

Citation:

Citation: Sterbova, Petra; Wang, Chun-Hsiung; Carillo, Kathleen; Lou, Yuan-Chao; Kato, Takayuki; Namba, Keiichi; Tzou, Der-Lii; Chang, Wei-Hau. "Molecular Mechanism of pH-Induced Protrusion Configuration Switching in Piscine Betanodavirus Implies a Novel Antiviral Strategy" ACS Infect. Dis. 10, 3304-3319 (2024).
PubMed: 39087906

Assembly members:

Assembly members:
entity_1, polymer, 125 residues, 13809.3 Da.

Natural source:

Natural source: Common Name: Dragon grouper nervous necrosis virus Taxonomy ID: 292633 Superkingdom: Viruses Kingdom: not available Genus/species: Betanodavirus Redspotted grouper nervous necrosis virus

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: TPEETTAPIMTQGSLYNDSL STNDFKSILLGSTPLDIAPD GAVFQLDRPLSIDYSLGTGD VDRAVYWHLKKFAGNAGTPA GWFRWGIWDNFNKTFTDGVA YYSDEQPRQILLPVGTVCTR VDSEN

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	376
15N chemical shifts	120
1H chemical shifts	120

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	protrusion domain, chain 1	1
2	protrusion domain, chain 2	1
3	protrusion domain, chain 3	1

Entities:

Entity 1, protrusion domain, chain 1 125 residues - 13809.3 Da.

1

THR

PRO

GLU

THR

ALA

PRO

ILE

MET

2

THR

GLN

GLY

SER

LEU

TYR

ASN

ASP

SER

LEU

3

SER

THR

ASN

ASP

PHE

LYS

SER

ILE

LEU

4

GLY

SER

THR

PRO

LEU

ASP

ILE

ALA

PRO

ASP

5

GLY

ALA

VAL

PHE

GLN

LEU

ASP

ARG

PRO

LEU

6

SER

ILE

ASP

TYR

SER

LEU

GLY

THR

GLY

ASP

7

VAL

ASP

ARG

ALA

VAL

TYR

TRP

HIS

LEU

LYS

8

LYS

PHE

ALA

GLY

ASN

ALA

GLY

THR

PRO

ALA

9

GLY

TRP

PHE

ARG

TRP

GLY

ILE

TRP

ASP

ASN

10

PHE

ASN

LYS

THR

PHE

THR

ASP

GLY

VAL

ALA

11

TYR

SER

ASP

GLU

GLN

PRO

ARG

GLN

ILE

12

LEU

PRO

VAL

GLY

THR

VAL

CYS

THR

ARG

13

VAL

ASP

SER

GLU

ASN

Samples:

sample_1: Protrusion domain, [U-13C; U-15N; U-2H], 1.0 mM; sodium acetate 20 mM; sodium chloride 50 mM; EDTA 0.5 mM; sodium azide 0.02%

sample_conditions_1: ionic strength: 0.07 M; pH: 5.0; pressure: 1 atm; temperature: 298 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 HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1

Software:

NMRViewJ - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III 850 MHz

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