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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
SampleChikungunya virus strain Senegal 37997
SourceChikungunya virus strain Senegal 37997 / virus
Map dataChikungunya virus strain Senegal 37997
Methodsingle particle reconstruction, at 6.8 Å resolution
AuthorsRossmann MG / Yap ML / Sakurai A / Ishikawa M / Rossmann MG / Akahata W
CitationProc. Natl. Acad. Sci. U.S.A., 2017

Proc. Natl. Acad. Sci. U.S.A., 2017 Yorodumi Papers
Structural studies of Chikungunya virus maturation.
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: Dec 6, 2017

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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
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5vu2
  • Imaged by Jmol
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3D viewer


View / / Stereo:
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Slabnear <=> far

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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
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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 package.

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 / virus
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 / virus
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 / virus
Strain: 37997

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Component #4: protein, capsid protein

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

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Experimental details

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Sample preparation

Specimen stateparticle
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 assessment)

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Atomic model buiding

Output model

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Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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