5MV2

Crystal structure of the E protein of the Japanese encephalitis live attenuated vaccine virus

PDB DOI: https://doi.org/10.2210/pdb5MV2/pdb

Classification: VIRAL PROTEIN
Organism(s): Japanese encephalitis virus strain SA-14
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2017-01-14 Released: 2018-05-23
Deposition Author(s): Liu, X., Zhao, X., Na, R., Li, L., Warkentin, E., Witt, J., Lu, X., Wei, Y., Peng, G., Li, Y., Wang, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.223
R-Value Work: 0.180
R-Value Observed: 0.182

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The structure differences of Japanese encephalitis virus SA14 and SA14-14-2 E proteins elucidate the virulence attenuation mechanism.

Liu, X., Zhao, X., Na, R., Li, L., Warkentin, E., Witt, J., Lu, X., Yu, Y., Wei, Y., Peng, G., Li, Y., Wang, J.

(2019) Protein Cell 10: 149-153

PubMed: 29752689 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1007/s13238-018-0551-6
Primary Citation of Related Structures:
5MV1, 5MV2

Organizational Affiliation

National Institutes for Food and Drug Control, Beijing, 102609, China.

Macromolecule Content

Total Structure Weight: 44.83 kDa
Atom Count: 3,338
Modelled Residue Count: 410
Deposited Residue Count: 416
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E protein	A	416	Japanese encephalitis virus strain SA-14	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P27395 (Japanese encephalitis virus (strain SA-14)) Explore P27395 Go to UniProtKB: P27395
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27395
Sequence AnnotationsExpand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.223
R-Value Work: 0.180
R-Value Observed: 0.182
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.6	α = 90
b = 55.9	β = 132.1
c = 90.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-05-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-23
Type: Initial release
Version 1.1: 2019-02-27
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary

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.

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