8R2L | pdb_00008r2l

Crystal structure of the ectodomain of TBEV E protein (Sofjin strain)

PDB DOI: https://doi.org/10.2210/pdb8R2L/pdb

Classification: VIRAL PROTEIN
Organism(s): Tick-borne encephalitis virus (STRAIN SOFJIN)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-06 Released: 2024-10-09
Deposition Author(s): Vlaskina, A.V., Samygina, V.R.
Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.286 (Depositor), 0.279 (DCC)
R-Value Work:
0.202 (Depositor), 0.205 (DCC)

Starting Model: experimental
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Literature

Self-Assembly and Conformational Change in the Oligomeric Structure of the Ectodomain of the TBEV E Protein Studied via X-ray, Small-Angle X-ray Scattering, and Molecular Dynamics

Konarev, P.V., Vlaskina, A.V., Korzhenevskiy, D., Rakitina, T.V., Petrenko, D., Agapova, Y., Kordonskaya, Y., Samygina, V.R.

(2023) Crystals (Basel)

DOI: https://doi.org/10.3390/cryst13121676

Macromolecule Content

Total Structure Weight: 43.39 kDa
Atom Count: 3,036
Modeled Residue Count: 394
Deposited Residue Count: 395
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein E	A [auth AAA]	395	Tick-borne encephalitis virus (STRAIN SOFJIN)	Mutation(s): 0
UniProt
Find proteins for P07720 (Tick-borne encephalitis virus Far Eastern subtype (strain Sofjin)) Explore P07720 Go to UniProtKB: P07720
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07720
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.286 (Depositor), 0.279 (DCC)
R-Value Work: 0.202 (Depositor), 0.205 (DCC)

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.061	α = 90
b = 165.061	β = 90
c = 165.061	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Higher Education of the Russian Federation	Russian Federation	--

Revision History (Full details and data files)

Version 1.0: 2024-10-09
Type: Initial release

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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.