BMRB Entry 34339

Name: Structure determination of N-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics
Published: 2019-03-15

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PDB ID: 6qan
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34339
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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:

Structure determination of N-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics

Deposition date:

2018-12-19

Original release date:

2019-03-15

Authors:

Karska, Natalia; Rodziewicz-Motowidlo, Sylwia

Citation:

Citation: Karska, N.; Graul, M.; Sikorska, E.; Zhukov, I.; Slusarz, M.; Kasprzykowski, F.; Lipinska, A.; Rodziewicz-Motowidlo, S.. "Structure determination of UL49.5 transmembrane protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics." Biochim Biophys Acta Biomembr 1861, 926-938 (2019).
PubMed: 30772281

Assembly members:

Assembly members:
Envelope glycoprotein N, polymer, 36 residues, 3825.316 Da.

Natural source:

Natural source: Common Name: Bovine alphaherpesvirus 1 Taxonomy ID: 10320 Superkingdom: Viruses Kingdom: not available Genus/species: Varicellovirus Bovine alphaherpesvirus 1

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Envelope glycoprotein N: RDPLLDAXRREGAXDFWSAG XYARGVPLSEPPQALX

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	218

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 36 residues - 3825.316 Da.

1

ARG

ASP

PRO

LEU

ASP

ALA

NLE

ARG

2

GLU

GLY

ALA

NLE

ASP

PHE

TRP

SER

ALA

GLY

3

ABA

TYR

ALA

ARG

GLY

VAL

PRO

LEU

SER

GLU

4

PRO

GLN

ALA

LEU

NH2

Samples:

sample_1: N.BHV 1.0 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 bar; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D TOCSY	sample_1	isotropic	sample_conditions_1
2D TOCSY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D ROESY	sample_1	isotropic	sample_conditions_1

Software:

SPARKY v3.114, Goddard - chemical shift assignment

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

SPARKY, Goddard - data analysis, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker AvanceIII 700 MHz
Varian Uniform NMR System 800 MHz