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- EMDB-22027: Reprocessing of EMPIAR-10184 data (aldolase) with particles picke... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-22027
TitleReprocessing of EMPIAR-10184 data (aldolase) with particles picked by Kpicker
Map data
SampleRabbit muscle aldolase
Function / homology
Function and homology information


negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / glycolytic process / protein homotetramerization / positive regulation of cell migration
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase-type TIM barrel
Similarity search - Domain/homology
Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsMcSweeney DM / McSweeney SM / Liu Q
CitationJournal: IUCrJ / Year: 2020
Title: A self-supervised workflow for particle picking in cryo-EM.
Authors: Donal M McSweeney / Sean M McSweeney / Qun Liu /
Abstract: High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an ...High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an iterative strategy, which uses a 2D class average to improve training particles, and a progressively improved convolutional neural network for particle picking. To automate the selection of particles, a threshold is defined (%/Res) using the ratio of percentage class distribution and resolution as a cutoff. This workflow has been tested using six publicly available data sets with different particle sizes and shapes, and can automatically pick particles with minimal user input. The picked particles support high-resolution reconstructions at 3.0 Å or better. This workflow is a step towards automated single-particle cryo-EM data analysis at the stage of particle picking. It may be used in conjunction with commonly used single-particle analysis packages such as , , , and .
History
DepositionMay 21, 2020-
Header (metadata) releaseAug 5, 2020-
Map releaseAug 5, 2020-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.212
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.212
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22027.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 224 pix.
= 191.52 Å
0.86 Å/pix.
x 224 pix.
= 191.52 Å
0.86 Å/pix.
x 224 pix.
= 191.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density
Contour LevelBy AUTHOR: 0.212 / Movie #1: 0.212
Minimum - Maximum-0.44240606 - 1.2215651
Average (Standard dev.)-0.0033534963 (±0.05516744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 191.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8550.8550.855
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z191.520191.520191.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ352352352
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.4421.222-0.003

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Supplemental data

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Sample components

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Entire Rabbit muscle aldolase

EntireName: Rabbit muscle aldolase / Number of Components: 1

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Component #1: protein, Rabbit muscle aldolase

ProteinName: Rabbit muscle aldolase / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 8
Support filmunspecified
VitrificationCryogen Name: ETHANE

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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: 65 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 114133
3D reconstructionResolution: 2.45 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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