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- EMDB-8508: Cryo-EM Structure of Immature Zika Virus -

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Basic information

Entry
Database: EMDB / ID: 8508
TitleCryo-EM Structure of Immature Zika Virus
SampleZika virus
SourceZika virus / virus / ジカウイルス
Map dataCryo-EM Reconstruction of Immature Zika Virus
Methodsingle particle (icosahedral) reconstruction, at 9.1 Å resolution
AuthorsMangala Prasad V / Miller AS
CitationNat. Struct. Mol. Biol., 2017, 24, 184-186

Nat. Struct. Mol. Biol., 2017, 24, 184-186 Yorodumi Papers
Structure of the immature Zika virus at 9 Å resolution.
Vidya Mangala Prasad / Andrew S Miller / Thomas Klose / Devika Sirohi / Geeta Buda / Wen Jiang / Richard J Kuhn / Michael G Rossmann

Validation ReportPDB-ID: 5u4w

SummaryFull reportAbout validation report
DateDeposition: Dec 6, 2016 / Header (metadata) release: Dec 21, 2016 / Map release: Jan 11, 2017 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 4.5
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5u4w
  • Surface level: 4.5
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5u4w
  • Imaged by Jmol
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Supplemental images

Downloads & links

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Map

Fileemd_8508.map.gz (map file in CCP4 format, 151733 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
336 pix
2.6 Å/pix.
= 873.6 Å
336 pix
2.6 Å/pix.
= 873.6 Å
336 pix
2.6 Å/pix.
= 873.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.6 Å
Density
Contour Level:4.5 (by author), 4.5 (movie #1):
Minimum - Maximum-32.93714 - 22.248032
Average (Standard dev.)0.055202045 (1.5859408)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions336336336
Origin-168-168-168
Limit167167167
Spacing336336336
CellA=B=C: 873.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.62.62.6
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z873.600873.600873.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-168-168-168
NC/NR/NS336336336
D min/max/mean-32.93722.2480.055

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Supplemental data

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Sample components

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Entire Zika virus

EntireName: Zika virus / Number of components: 8

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Component #1: virus, Zika virus

VirusName: Zika virus / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Zika virus / virus / ジカウイルス
Source (natural)Host Species: Homo sapiens / human
Shell #1Name of element: prM-E glycoprotein / Diameter: 600 Å / T number(triangulation number): 1

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Component #2: protein, Transmembrane domains

ProteinName: Transmembrane domains / Recombinant expression: No
SourceSpecies: Zika virus / virus / ジカウイルス

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Component #3: protein, E protein

ProteinName: E protein / Recombinant expression: No
MassTheoretical: 44.80141 kDa
Source (engineered)Expression System: Zika virus / virus / ジカウイルス

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Component #4: protein, pr domain

ProteinName: pr domain / Recombinant expression: No
MassTheoretical: 9.261531 kDa
Source (engineered)Expression System: Zika virus / virus / ジカウイルス

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Component #5: protein, Protein E

ProteinName: Protein E / Recombinant expression: No
MassTheoretical: 6.892228 kDa
SourceSpecies: Zika virus / virus / ジカウイルス

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Component #6: protein, M protein

ProteinName: M protein / Recombinant expression: No
MassTheoretical: 5.984065 kDa
SourceSpecies: Zika virus / virus / ジカウイルス

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Component #7: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINE / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #8: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 8
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 %

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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: 4.7 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3341

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 9315
3D reconstructionAlgorithm: FOURIER SPACE / Software: jspr / Resolution: 9.1 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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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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