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- EMDB-5474: Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likel... -

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Basic information

Entry
Database: EMDB / ID: EMD-5474
TitleDynamics in Cryo EM Reconstructions Visualized with Maximum-Likelihood Derived Variance Maps
Map dataCryo-EM reconstruction of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
Sample
  • Sample: Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
  • Virus: Nudaurelia capensis omega virus
Keywordstime-resolved / single particle reconstruction / virus maturation / protein folding / quasi-equivalence / cryo electron microscopy / Nudaurelia Capensis Omega Virus / maximum likelihood estimation / expectation maximization algorithm / heterogeneous particles / variance map
Biological speciesNudaurelia capensis omega virus
Methodsingle particle reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsWang Q / Matsui T / Domitrovic T / Zheng Y / Doerschuk PC / Johnson JE
CitationJournal: J Struct Biol / Year: 2013
Title: Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps.
Authors: Qiu Wang / Tsutomu Matsui / Tatiana Domitrovic / Yili Zheng / Peter C Doerschuk / John E Johnson /
Abstract: CryoEM data capture the dynamic character associated with biological macromolecular assemblies by preserving the various conformations of the individual specimens at the moment of flash freezing. ...CryoEM data capture the dynamic character associated with biological macromolecular assemblies by preserving the various conformations of the individual specimens at the moment of flash freezing. Regions of high variation in the data set are apparent in the image reconstruction due to the poor density that results from the lack of superposition of these regions. These observations are qualitative and, to date, only preliminary efforts have been made to quantitate the heterogeneity in the ensemble of particles that are individually imaged. We developed and tested a quantitative method for simultaneously computing a reconstruction of the particle and a map of the space-varying heterogeneity of the particle based on an entire data set. The method uses a maximum likelihood algorithm that explicitly takes into account the continuous variability from one instance to another instance of the particle. The result describes the heterogeneity of the particle as a variance to be plotted at every voxel of the reconstructed density. The test, employing time resolved data sets of virus maturation, not only recapitulated local variations obtained with difference map analysis, but revealed a remarkable time dependent reduction in the overall particle dynamics that was unobservable with classical methods of analysis.
History
DepositionAug 19, 2012-
Header (metadata) releaseOct 2, 2013-
Map releaseOct 2, 2013-
UpdateOct 2, 2013-
Current statusOct 2, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0001
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0001
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5474.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
Voxel sizeX=Y=Z: 2.768 Å
Density
Contour LevelBy AUTHOR: 0.0001 / Movie #1: 0.0001
Minimum - Maximum-0.00089469 - 0.0009674
Average (Standard dev.)0.0000192 (±0.00016826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 553.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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-0.0010.0010.000

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Supplemental data

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Sample components

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Entire : Nudaurelia capensis omega virus (NwV) capsid at 30min time point ...

EntireName: Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
Components
  • Sample: Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
  • Virus: Nudaurelia capensis omega virus

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Supramolecule #1000: Nudaurelia capensis omega virus (NwV) capsid at 30min time point ...

SupramoleculeName: Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
type: sample / ID: 1000 / Oligomeric state: Icosahedral virus / Number unique components: 1

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Supramolecule #1: Nudaurelia capensis omega virus

SupramoleculeName: Nudaurelia capensis omega virus / type: virus / ID: 1 / Name.synonym: NwV (N omega V) / NCBI-ID: 12541 / Sci species name: Nudaurelia capensis omega virus / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: NwV (N omega V)
Host (natural)Organism: Lepidoptera (butterflies and moths) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Diameter: 400 Å / T number (triangulation number): 4

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateFeb 13, 2008
Image recordingDetails: Data were collected using the Leginon automated electron microscopy package and data processing was performed using the Appion pipeline.
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each image
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 1200
DetailsThe reconstruction uses a maximum likelihood algorithm that explicitly takes into account the continuous variability from one instance to another instance of the particle.

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