BMRB Entry 27728

Name: Structure determination of N-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics
Published: 2019-02-25

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27728

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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:

2018-12-14

Original release date:

2019-02-25

Authors:

Karska, Natalia; Graul, Malgorzata; Sikorska, Emilia; Zhukov, Igor; Slusarz, Magdalena; Kasprzykowski, Franciszek; Lipinska, Andrea; Rodziewicz-Motowidlo, Sylwia

Citation:

Citation: Karska, Natalia; Graul, Malgorzata; Sikorska, Emilia; Zhukov, Igor; Slusarz, Magdalena; Kasprzykowski, Franciszek; Lipinska, Andrea; Rodziewicz-Motowidlo, Sylwia. "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:
N.BHV, polymer, 35 residues, 3819 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
N.BHV: RDPLLDAXRREGAXDFWSAG XYARGVPLSEPPQAL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_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	N.BHV	1

Entities:

Entity 1, N.BHV 35 residues - 3819 Da.

This is the N-terminal domain of a transmembrane protein

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

Samples:

sample_1: N.BHV 4.8 mM; DPC 100 mM; Acetic Acid-d4 0.02 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.05 M; pH: 5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H ROESY	sample_1	isotropic	sample_conditions_1

Software:

SPARKY v3, Goddard - chemical shift assignment, chemical shift calculation, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - data analysis, structure solution

AMBER v15, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - geometry optimization, refinement, structure solution

NMR spectrometers:

Bruker Avance 700 MHz
Agilent Uniform NMR System 800 MHz