BMRB Entry 34709

Name: Solution structure of homodimeric Capsid protein (residues 17-95) of Tick-borne encephalitis virus (d16-TBEVC)
Published: 2022-10-14

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PDB ID: 7ywq
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34709
MolProbity Validation Chart

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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 homodimeric Capsid protein (residues 17-95) of Tick-borne encephalitis virus (d16-TBEVC)

Deposition date:

2022-02-14

Original release date:

2022-10-14

Authors:

Novotny, R.

Citation:

Citation: Selinger, Martin; Novotny, Radim; Sys, Jakub; Roby, Justin; Tykalova, Hana; Ranjani, Ganji Sri; Vancova, Marie; Jaklova, Katerina; Kaufman, Filip; Bloom, Marshall; Zdrahal, Zbynek; Grubhoffer, Libor; Forwood, Jade; Hrabal, Richard; Rumlova, Michaela; Sterba, Jan. "Tick-borne encephalitis virus capsid protein induces translational shutoff as revealed by its structural-biological analysis" J. Biol. Chem. 298, 102585-102585 (2022).
PubMed: 36223838

Assembly members:

Assembly members:
entity_1, polymer, 79 residues, 8869.752 Da.

Natural source:

Natural source: Common Name: Tick-borne encephalitis virus Taxonomy ID: 11084 Superkingdom: Viruses Kingdom: not available Genus/species: Flavivirus Tick-borne encephalitis virus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: pET22B

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: VSKETATKTRQPRVQMPNGL VLMRMMGILWHAVAGTARNP VLKAFWNSVPLKQATAALRK IKRTVSALMVGLQKRGKRR

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	247
15N chemical shifts	58
1H chemical shifts	394

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1

Entities:

Entity 1, unit_1 79 residues - 8869.752 Da.

1

VAL

SER

LYS

GLU

THR

ALA

THR

LYS

THR

ARG

2

GLN

PRO

ARG

VAL

GLN

MET

PRO

ASN

GLY

LEU

3

VAL

LEU

MET

ARG

MET

GLY

ILE

LEU

TRP

4

HIS

ALA

VAL

ALA

GLY

THR

ALA

ARG

ASN

PRO

5

VAL

LEU

LYS

ALA

PHE

TRP

ASN

SER

VAL

PRO

6

LEU

LYS

GLN

ALA

THR

ALA

LEU

ARG

LYS

7

ILE

LYS

ARG

THR

VAL

SER

ALA

LEU

MET

VAL

8

GLY

LEU

GLN

LYS

ARG

GLY

LYS

ARG

Samples:

sample_1: d16-TBEVC, [U-99% 13C; U-99% 15N], 0.4 mM; NaCl, none, 50 mM; sodium phosphate, none, 50 mM; glycerol, none, 5%

sample_conditions_1: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HCACO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

TopSpin v3.5, Bruker Biospin - collection, processing

CcpNmr Analysis v2.5.2, CCPN - chemical shift assignment, data analysis, peak picking

X-PLOR NIH v3.2, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

HADDOCK v2.2, Bonvin - processing

NMR spectrometers:

Bruker AVANCE 600 MHz

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