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- EMDB-3771: Three-dimensional reconstruction of FLiP virion -

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Basic information

Entry
Database: EMDB / ID: 3771
TitleThree-dimensional reconstruction of FLiP virion
Sampleunidentified phage
Sourceunidentified phage / virus
Map dataReconstruction of Flavobacterium infecting lipid-containing phage FLiP
Methodsingle particle (icosahedral) reconstruction, at 4 Å resolution
AuthorsDe Colibus L / Gillum A / Stuart DI / Huiskonen JT
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 8378-8383

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 8378-8383 StrPapers
Virus found in a boreal lake links ssDNA and dsDNA viruses.
Elina Laanto / Sari Mäntynen / Luigi De Colibus / Jenni Marjakangas / Ashley Gillum / David I Stuart / Janne J Ravantti / Juha T Huiskonen / Lotta-Riina Sundberg

Validation ReportPDB-ID: 5oac

SummaryFull reportAbout validation report
DateDeposition: Jun 21, 2017 / Header (metadata) release: Jul 5, 2017 / Map release: Jul 26, 2017 / Last update: Aug 9, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5oac
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5oac
  • Imaged by Jmol
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3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3771.map.gz (map file in CCP4 format, 1372001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
700 pix
1.35 Å/pix.
= 945. Å
700 pix
1.35 Å/pix.
= 945. Å
700 pix
1.35 Å/pix.
= 945. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.08169098 - 0.16613102
Average (Standard dev.)0.0012641506 (0.0115462085)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions700700700
Origin-349-349-349
Limit350350350
Spacing700700700
CellA=B=C: 945 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z700700700
origin x/y/z0.0000.0000.000
length x/y/z945.000945.000945.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-349-349-349
NC/NR/NS700700700
D min/max/mean-0.0820.1660.001

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Supplemental data

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Mask #1

Fileemd_3771_msk_1.map ( map file in CCP4 format, 1372001 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsmask used for FSC
Space group number1

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Mask #1~

Fileemd_3771_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire unidentified phage

EntireName: unidentified phage
Details: Flavobacterium infecting lipid-containing phage FLiP
Number of components: 2

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Component #1: virus, unidentified phage

VirusName: unidentified phage / Class: VIRION
Details: Flavobacterium infecting lipid-containing phage FLiP
Empty: No / Enveloped: Yes / Isolate: SPECIES
SpeciesSpecies: unidentified phage / virus
Source (natural)Host Species: Flavobacterium / bacteria / Host species strain: sp B330
Shell #1Name of element: Capsid / Diameter: 550 Å / T number(triangulation number): 25

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Component #2: protein, Major capsid protein

ProteinName: Major capsid protein / Recombinant expression: No
MassTheoretical: 34.533934 kDa
SourceSpecies: unidentified phage / virus

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 20 mM PBS / pH: 7.2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 22 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 160000 X (nominal), 37037 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 5 microns

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 934
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 4 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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