- EMDB-5471: Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likel... -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-5471
Title
Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likelihood Derived Variance Maps
Map data
Cryo-EM reconstruction of the structure standard deviation of Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
Sample
Sample: Cryo-EM reconstruction of the structure variance of Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
Virus: Nudaurelia capensis omega virus
Keywords
time-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
Journal: 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
Deposition
Aug 19, 2012
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Header (metadata) release
Oct 2, 2013
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Map release
Oct 2, 2013
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Update
Oct 2, 2013
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Current status
Oct 2, 2013
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_5471.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Cryo-EM reconstruction of the structure standard deviation of Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
Voxel size
X=Y=Z: 2.768 Å
Density
Contour Level
By AUTHOR: 0.00000009 / Movie #1: 1.0E-7
Minimum - Maximum
0.0 - 0.00000727
Average (Standard dev.)
0.00000002 (±0.00000004)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
-100
-100
-100
Dimensions
200
200
200
Spacing
200
200
200
Cell
A=B=C: 553.6 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.768
2.768
2.768
M x/y/z
200
200
200
origin x/y/z
0.000
0.000
0.000
length x/y/z
553.600
553.600
553.600
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-150
-150
0
NX/NY/NZ
301
301
151
MAP C/R/S
1
2
3
start NC/NR/NS
-100
-100
-100
NC/NR/NS
200
200
200
D min/max/mean
0.000
0.000
0.000
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Supplemental data
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Sample components
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Entire : Cryo-EM reconstruction of the structure variance of Nudaurelia ca...
Entire
Name: Cryo-EM reconstruction of the structure variance of Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
Components
Sample: Cryo-EM reconstruction of the structure variance of Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
Virus: Nudaurelia capensis omega virus
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Supramolecule #1000: Cryo-EM reconstruction of the structure variance of Nudaurelia ca...
Supramolecule
Name: Cryo-EM reconstruction of the structure variance of Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation type: sample / ID: 1000 / Oligomeric state: Icosahedral virus / Number unique components: 1
Organism: Lepidoptera (butterflies and moths) / synonym: INVERTEBRATES
Virus shell
Shell ID: 1 / Diameter: 400 Å / T number (triangulation number): 4
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Vitrification
Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK I
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Electron microscopy
Microscope
FEI TECNAI F20
Date
Feb 13, 2008
Image recording
Details: Data were collected using the Leginon automated electron microscopy package and data processing was performed using the Appion pipeline.
Electron beam
Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stage
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
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Image processing
Details
The reconstruction uses a maximum likelihood algorithm that explicitly takes into account the continuous variability from one instance to another instance of the particle.
CTF correction
Details: Each image
Final reconstruction
Algorithm: OTHER / Number images used: 1200
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