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- EMDB-8734: Electron cryo-microscopy of "immature" Chikungunya VLP -

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Basic information

Entry
Database: EMDB / ID: 8734
TitleElectron cryo-microscopy of "immature" Chikungunya VLP
Map dataChikungunya virus strain Senegal 37997
SampleChikungunya virus strain Senegal 37997:
virus / (E1 envelope glycoprotein) x 2 / E3 envelope glycoprotein / capsid proteinCapsid / E2 envelope glycoprotein
Function / homologyAlphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set ...Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set / Peptidase S1, PA clan / Alphavirus E1 glycoprotein / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Peptidase S3, togavirin / Togavirin / T=4 icosahedral viral capsid / host cell membrane / viral capsid / fusion of virus membrane with host endosome membrane / host cell cytoplasm / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / Structural polyprotein / Structural polyprotein / Structural polyprotein
Function and homology information
SourceChikungunya virus strain Senegal 37997
Methodsingle particle reconstruction / cryo EM / 6.8 Å resolution
AuthorsRossmann MG / Yap ML / Sakurai A / Ishikawa M / Rossmann MG / Akahata W
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural studies of Chikungunya virus maturation.
Authors: Moh Lan Yap / Thomas Klose / Akane Urakami / S Saif Hasan / Wataru Akahata / Michael G Rossmann
Validation ReportPDB-ID: 5vu2

SummaryFull reportAbout validation report
DateDeposition: May 18, 2017 / Header (metadata) release: Aug 23, 2017 / Map release: Dec 6, 2017 / Last update: Jan 3, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5vu2
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5vu2
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8734.map.gz (map file in CCP4 format, 1811940 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
768 pix
1.3 Å/pix.
= 998.4 Å
768 pix
1.3 Å/pix.
= 998.4 Å
768 pix
1.3 Å/pix.
= 998.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-5 - 5
Average (Standard dev.)0.029038956 (0.4375374)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions768768768
Origin-384-384-384
Limit383383383
Spacing768768768
CellA=B=C: 998.39996 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z768768768
origin x/y/z0.0000.0000.000
length x/y/z998.400998.400998.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-384-384-384
NC/NR/NS768768768
D min/max/mean-5.0005.0000.029

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Supplemental data

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Sample components

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Entire Chikungunya virus strain Senegal 37997

EntireName: Chikungunya virus strain Senegal 37997 / Number of components: 6

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Component #1: virus, Chikungunya virus strain Senegal 37997

VirusName: Chikungunya virus strain Senegal 37997 / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Chikungunya virus strain Senegal 37997
Source (engineered)Expression System: Homo sapiens (human) / Vector: pUC119 / Cell of expression system: Human embryonic kidney

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Component #2: protein, E1 envelope glycoprotein

ProteinName: E1 envelope glycoprotein / Recombinant expression: No
MassTheoretical: 95.538164 kDa
Source (engineered)Expression System: Chikungunya virus strain Senegal 37997 / Strain: 37997

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Component #3: protein, E3 envelope glycoprotein

ProteinName: E3 envelope glycoprotein / Recombinant expression: No
MassTheoretical: 6.92699 kDa
Source (engineered)Expression System: Chikungunya virus strain Senegal 37997 / Strain: 37997

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Component #4: protein, capsid protein

ProteinName: capsid proteinCapsid / Recombinant expression: No
MassTheoretical: 16.229508 kDa
Source (engineered)Expression System: Chikungunya virus (strain 37997) / Strain: 37997

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Component #5: protein, E1 envelope glycoprotein

ProteinName: E1 envelope glycoprotein / Recombinant expression: No
MassTheoretical: 4.810723 kDa
Source (engineered)Expression System: Chikungunya virus strain Senegal 37997 / Strain: 37997

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Component #6: protein, E2 envelope glycoprotein

ProteinName: E2 envelope glycoprotein / Recombinant expression: No
MassTheoretical: 8.817458 kDa
Source (engineered)Expression System: Chikungunya virus strain Senegal 37997 / Strain: 37997

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/ml / pH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 36 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 72944
3D reconstructionSoftware: jspr / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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