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

Open data

ID or keywords:


Basic information

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 .
DepositionMay 21, 2020-
Header (metadata) releaseAug 5, 2020-
Map releaseAug 5, 2020-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing site: RCSB / Status: Released

Structure visualization

  • 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:
Supplemental images

Downloads & links


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

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
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


Map geometry
Axis orderXYZ
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
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.4421.222-0.003

Supplemental data

Sample components

Entire Rabbit muscle aldolase

EntireName: Rabbit muscle aldolase / Number of Components: 1

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)

Experimental details

Sample preparation

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

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)

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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