8ECH | pdb_00008ech

Tick-borne encephalitis virus capsid protein NLS bound to host importin alpha 2

PDB DOI: https://doi.org/10.2210/pdb8ECH/pdb

Classification: VIRAL PROTEIN
Organism(s): Tick-borne encephalitis virus, Mus musculus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-09-02 Released: 2022-09-14
Deposition Author(s): Roby, J.A., Forwood, J.K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.219 (Depositor), 0.218 (DCC)
R-Value Work:
0.193 (Depositor), 0.196 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Structure and biological functions of tick-borne encephalitis virus capsid protein

Selinger, M., Novotny, R., Sys, J., Roby, J.A., Tykalova, H., Ranjani, G.S., Vancova, M., Jaklova, K., Kaufman, F., Bloom, M.E., Zdrahal, Z., Grubhoffer, L., Forwood, J.K., Hrabal, R., Rumlova, M., Sterba, J.

To be published.

Macromolecule Content

Total Structure Weight: 57.85 kDa
Atom Count: 3,507
Modeled Residue Count: 437
Deposited Residue Count: 532
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein C	A [auth C]	22	Tick-borne encephalitis virus	Mutation(s): 0
UniProt
Find proteins for Q01299 (Tick-borne encephalitis virus (strain Hypr)) Explore Q01299 Go to UniProtKB: Q01299
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01299
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Importin subunit alpha-1	B [auth E]	510	Mus musculus	Mutation(s): 0 Gene Names: Kpna2, Rch1
UniProt & NIH Common Fund Data Resources
Find proteins for P52293 (Mus musculus) Explore P52293 Go to UniProtKB: P52293
IMPC: MGI:103561
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52293
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.219 (Depositor), 0.218 (DCC)
R-Value Work: 0.193 (Depositor), 0.196 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.209	α = 90
b = 90.05	β = 90
c = 99.218	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-09-14
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.