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- EMDB-20091: Singapore Grouper Iridovirus (SGIV) at 8.6 Angstrom Resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-20091
TitleSingapore Grouper Iridovirus (SGIV) at 8.6 Angstrom Resolution
Map data
SampleSingapore grouper iridovirus:
virus / Major capsid protein
Function / homology
Function and homology information


viral capsid / structural molecule activity
Major capsid protein, C-terminal / Hexon coat protein, subdomain 4 / Group II dsDNA virus coat/capsid protein / Major capsid protein, N-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Major capsid protein N-terminus
Major capsid protein
Biological speciesSingapore grouper iridovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsPintilie G / Chen D-H / Tran BN / Jakana J / Wu J / Hew CL / Chiu W
CitationJournal: To be Published
Title: Segmentation and Comparative Modeling in a 8.6 Angstrom Cryo-EM Map of the 220 nm Diameter Singapore Grouper Iridovirus
Authors: Pintilie G / Chen D-H / Tran BN / Jakana J / Wu J / Hew CL / Chiu W
Validation ReportPDB-ID: 6ojn

SummaryFull reportAbout validation report
DateDeposition: Apr 11, 2019 / Header (metadata) release: Jun 12, 2019 / Map release: Jun 12, 2019 / Update: Jun 12, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ojn
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20091.map.gz / Format: CCP4 / Size: 6.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.37 Å/pix.
x 1200 pix.
= 2844. Å
2.37 Å/pix.
x 1200 pix.
= 2844. Å
2.37 Å/pix.
x 1200 pix.
= 2844. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.37 Å
Density
Contour LevelBy AUTHOR: 0.15 / Movie #1: 4
Minimum - Maximum-13.887831 - 21.549627000000001
Average (Standard dev.)-0.04749717 (±1.4707036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-600-600-600
Dimensions120012001200
Spacing120012001200
CellA=B=C: 2843.9998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.372.372.37
M x/y/z120012001200
origin x/y/z0.0000.0000.000
length x/y/z2844.0002844.0002844.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-600-600-600
NC/NR/NS120012001200
D min/max/mean-13.88821.550-0.047

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Supplemental data

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Sample components

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Entire Singapore grouper iridovirus

EntireName: Singapore grouper iridovirus / Number of components: 2

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Component #1: virus, Singapore grouper iridovirus

VirusName: Singapore grouper iridovirus / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: SPECIES
SpeciesSpecies: Singapore grouper iridovirus
Source (natural)Host Species: Epinephelus tauvina (greasy grouper)
Shell #1Name of element: Outer coat / Diameter: 2200.0 Å / T number (triangulation number): 247

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Component #2: protein, Major capsid protein

ProteinName: Major capsid protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 50.573141 kDa
SourceSpecies: Singapore grouper iridovirus

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: Blotted for 1 second before plunging..

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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: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 63290.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 15 µm

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 9422
3D reconstructionAlgorithm: FOURIER SPACE / Software: EMAN / Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Z-score of Cross Correlation scores / Refinement space: REAL
Input PDB model: 1M3Y
Output model

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