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- EMDB-5428: Cryo-EM reconstruction of Nudaurelia capensis omega virus (NwV) c... -

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Basic information

Entry
Database: EMDB / ID: 5428
TitleCryo-EM reconstruction of Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
KeywordsTime-resolved / T=4 / quasi-equivalence / maturation
SampleNudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
SourceNudaurelia capensis omega virus / virus / NwV (N omega V)
Map dataReconstruction of Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
Methodsingle particle (icosahedral) reconstruction, at 8.3 A resolution
AuthorsMatsui T / Lander GC / Khayat R / Johnson JE
CitationProc. Natl. Acad. Sci. U.S.A., 2010, 107, 14111-14115

Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 14111-14115 StrPapers
Subunits fold at position-dependent rates during maturation of a eukaryotic RNA virus.
Tsutomu Matsui / Gabriel C Lander / Reza Khayat / John E Johnson

DateDeposition: May 29, 2012 / Header (metadata) release: Jun 4, 2012 / Map release: Jun 4, 2012 / Last update: May 29, 2012

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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
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5428.map.gz (map file in CCP4 format, 31251 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
2.77 A/pix
= 553.6 A
200 pix
2.77 A/pix
= 553.6 A
200 pix
2.77 A/pix
= 553.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.768 A
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-4.57011175 - 7.01301813
Average (Standard dev.)0E-8 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-100-100-100
Limit999999
Spacing200200200
CellA=B=C: 553.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.7682.7682.768
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z553.600553.600553.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-4.5707.013-0.000

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Supplemental data

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Sample components

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Entire Nudaurelia capensis omega virus (NwV) capsid at 4hr time point fo...

EntireName: Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
Number of components: 1 / Oligomeric State: Icosahedral virus

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Component #1: virus, Nudaurelia capensis omega virus

VirusName: Nudaurelia capensis omega virus / a.k.a: NwV (N omega V) / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Nudaurelia capensis omega virus / virus / NwV (N omega V)
Source (natural)Host Species: Lepidoptera / Host category: INVERTEBRATES

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 10 mg/ml / Buffer solution: 100mM NaOAc, 250mM NaCl / pH: 5
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 % / Method: Blot for 5sec before plunging

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Date: Feb 13, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 16.5 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN

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Image acquisition

Image acquisition
295
Image acquisition
Datawereco llectedusi ngtheLegin onautomate delectronm icroscopyp ackageandd ataprocess ingwasperf ormedusing theAppionp ipeline

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 23392 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Projection matching / Software: EMAN / CTF correction: Each image
Details: Data processing was performed using the Appion pipeline.
Resolution: 8.3 A / Resolution method: FSC 0.5

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