BMRB Entry 27730

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

Click here to enlarge.

PDB ID: 6qbj
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27730
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

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

Deposition date:

2018-12-16

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:
TMC.BHV, polymer, 40 residues, 4209 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):
TMC.BHV: VVFYVALTAVXVAVALYAYG LXFRLXGASGPNKKESRGRG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	256

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	TMC.BHV	1

Entities:

Entity 1, TMC.BHV 40 residues - 4209 Da.

1	VAL	VAL	PHE	TYR	VAL	ALA	LEU	THR	ALA	VAL
2	NLE	VAL	ALA	VAL	ALA	LEU	TYR	ALA	TYR	GLY
3	LEU	ABA	PHE	ARG	LEU	NLE	GLY	ALA	SER	GLY
4	PRO	ASN	LYS	LYS	GLU	SER	ARG	GLY	ARG	GLY

Samples:

sample_1: TMC.BHV 2.7 mM; DPC 100 mM; Acetic Acid-d4 0.01 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

1	VAL	VAL	PHE	TYR	VAL	ALA	LEU	THR	ALA	VAL
2	NLE	VAL	ALA	VAL	ALA	LEU	TYR	ALA	TYR	GLY
3	LEU	ABA	PHE	ARG	LEU	NLE	GLY	ALA	SER	GLY
4	PRO	ASN	LYS	LYS	GLU	SER	ARG	GLY	ARG	GLY

1	VAL	VAL	PHE	TYR	VAL	ALA	LEU	THR	ALA	VAL
2	NLE	VAL	ALA	VAL	ALA	LEU	TYR	ALA	TYR	GLY
3	LEU	ABA	PHE	ARG	LEU	NLE	GLY	ALA	SER	GLY
4	PRO	ASN	LYS	LYS	GLU	SER	ARG	GLY	ARG	GLY

1	VAL	VAL	PHE	TYR	VAL	ALA	LEU	THR	ALA	VAL
2	NLE	VAL	ALA	VAL	ALA	LEU	TYR	ALA	TYR	GLY
3	LEU	ABA	PHE	ARG	LEU	NLE	GLY	ALA	SER	GLY
4	PRO	ASN	LYS	LYS	GLU	SER	ARG	GLY	ARG	GLY