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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 Å resolution / Particle / 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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 7, 2016 / Release: May 17, 2017

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Structure visualization

Movie
  • 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

Cellular component

Molecular function

Biological process

#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 experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Japanese encephalitis virus / Type: VIRUS / Entity ID: 1, 2 / Source: RECOMBINANT
Molecular weightValue: 11.8 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Japanese encephalitis virus / Strain: P3
Source (recombinant)Cell: vero / Organism: Chlorocebus aethiops / Plasmid: no plasmids
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Envelope protein / Diameter: 500 Å / Triangulation number (T number): 3
Buffer solutionDetails: PBS buffer / pH: 7.4
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 kelvins / Details: blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
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 / Calibrated defocus min: 1200 nm / Calibrated defocus max: 3000 nm / Cs: 2 mm / C2 aperture diameter: 100 mm
Specimen holderSpecimen holder model: OTHER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 1.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 5 / Number of real images: 2500
Image scansDimension width: 3710 / Dimension height: 3710 / Movie frames/image: 25 / Used frames/image: 2-18

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Processing

SoftwareName: PHENIX / Version: 1.10_2155: / Classification: refinement
EM software
IDNameVersionCategoryDetailsImaging IDImage processing IDFitting ID
2EMAN2.0IMAGE ACQUISITIONEMAN2 e2boxer.py was used to automatically select particle images1
3Relion1.3IMAGE ACQUISITIONRelion was used to reconstruct 3D structures1
5Gctf5.0CTF CORRECTION1
8CHIMERA2.0MODEL FITTING1
10RelionINITIAL EULER ASSIGNMENT1
11Relion1.3FINAL EULER ASSIGNMENT1
12Relion1.3CLASSIFICATION1
13Relion1.3RECONSTRUCTION1
14PHENIX3.OMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 22000
SymmetryPoint symmetry: I
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 15260 / Number of class averages: 120 / Symmetry type: POINT
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 / Pdb chain residue range: 1-395
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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