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- PDB-5wsn: Structure of Japanese encephalitis virus -

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Basic information

Entry
Database: PDB / ID: 5wsn
TitleStructure of Japanese encephalitis virus
DescriptorE protein, M protein
KeywordsVIRUS / Japanese encephalitis virus / Viral entry / Flavivirus / Neurotropism
Specimen sourceJapanese encephalitis virus / virus / 日本脳炎ウイルス
MethodElectron microscopy (4.3 A resolution / Single particle)
AuthorsWang, X. / Zhu, L. / Li, S. / Yuan, S. / Qin, C. / Fry, E.E. / Stuart, I.D. / Rao, Z.
CitationNat Commun, 2017, 8, 14-14

Nat Commun, 2017, 8, 14-14 StrPapers
Near-atomic structure of Japanese encephalitis virus reveals critical determinants of virulence and stability.
Xiangxi Wang / Shi-Hua Li / Ling Zhu / Qing-Gong Nian / Shuai Yuan / Qiang Gao / Zhongyu Hu / Qing Ye / Xiao-Feng Li / Dong-Yang Xie / Neil Shaw / Junzhi Wang / Thomas S Walter / Juha T Huiskonen / Elizabeth E Fry / Cheng-Feng Qin / David I Stuart / Zihe Rao

DateDeposition: Dec 7, 2016 / Release: May 17, 2017

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Biological unit as hexameric
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-6685
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Assembly

Deposited unit
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein


Theoretical massNumber of molelcules
Total (without water)185,2786
Polyers185,2786
Non-polymers00
Water0
#1
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
x 60


Theoretical massNumber of molelcules
Total (without water)11,116,651360
Polyers11,116,651360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#3
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
x 5


  • icosahedral pentamer
  • 926 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)926,38830
Polyers926,38830
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
x 6


  • icosahedral 23 hexamer
  • 1.11 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,111,66536
Polyers1,111,66536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
#5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
#6
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
x 60


  • crystal asymmetric unit, crystal frame
  • 11.1 MDa, 360 polymers
Theoretical massNumber of molelcules
Total (without water)11,116,651360
Polyers11,116,651360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60

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Components

#1: Polypeptide(L)E protein


Mass: 53508.684 Da / Num. of mol.: 3
Source: (gene. exp.) Japanese encephalitis virus / virus / 日本脳炎ウイルス
References: UniProt: A1E4C6
#2: Polypeptide(L)M protein


Mass: 8250.488 Da / Num. of mol.: 3
Source: (gene. exp.) Japanese encephalitis virus / virus / 日本脳炎ウイルス
References: UniProt: Q82863
Sequence detailsThis sequence is derived from Japanese encephalitis virus (P3 strain).

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Japanese encephalitis virus / Type: VIRUS
Details of the virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Buffer solutionDetails: PBS buffer
Specimen supportGrid material: COPPER / Grid mesh size: 400 /inch. / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 / Details: blot for 3 seconds before plunging

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Electron microscopy imaging

MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderSpecimen holder model: OTHER

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Processing

SoftwareName: PHENIX / Version: 1.10_2155: / Classification: refinement
ComputingStructure refinement: PHENIX (1.10_2155: phenix.real_space_refine)
3D reconstructionResolution: 4.3 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 15260 / Number of class averages: 120
Atomic model buildingOverall b value: 120 / Ref protocol: AB INITIO MODEL / Ref space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 3J57
Pdb chain id: A
Refine LS restraints
Refine idTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01113367
ELECTRON MICROSCOPYf_angle_d1.08018150
ELECTRON MICROSCOPYf_dihedral_angle_d8.96110527
ELECTRON MICROSCOPYf_chiral_restr0.0512075
ELECTRON MICROSCOPYf_plane_restr0.0062297

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