5MV2 | pdb_00005mv2

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1007/s13238-018-0551-6
• Primary Citation of Related Structures:  
  5MV1, 5MV2

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Organizational Affiliation: 
• National Institutes for Food and Drug Control, Beijing, 102609, China.
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany.
State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany. [e-mail].
National Institutes for Food and Drug Control, Beijing, 102609, China. [e-mail].
State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China. [e-mail].
National Institutes for Food and Drug Control, Beijing, 102609, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

• 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