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- EMDB-21492: Rabbit muscle aldolase cryo-EM structure using automatic preproce... -

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Basic information

Database: EMDB / ID: EMD-21492
TitleRabbit muscle aldolase cryo-EM structure using automatic preprocessing workflow
Map data
SampleRabbit muscle aldolase
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCianfrocco MA / Li Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-DBI-ABI 1759826 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01-CA-221289 United States
CitationJournal: Structure / Year: 2020
Title: High-Throughput Cryo-EM Enabled by User-Free Preprocessing Routines.
Authors: Yilai Li / Jennifer N Cash / John J G Tesmer / Michael A Cianfrocco /
Abstract: Single-particle cryoelectron microscopy (cryo-EM) continues to grow into a mainstream structural biology technique. Recent developments in data collection strategies alongside new sample preparation ...Single-particle cryoelectron microscopy (cryo-EM) continues to grow into a mainstream structural biology technique. Recent developments in data collection strategies alongside new sample preparation devices herald a future where users will collect multiple datasets per microscope session. To make cryo-EM data processing more automatic and user-friendly, we have developed an automatic pipeline for cryo-EM data preprocessing and assessment using a combination of deep-learning and image-analysis tools. We have verified the performance of this pipeline on a number of datasets and extended its scope to include sample screening by the user-free assessment of the qualities of a series of datasets under different conditions. We propose that our workflow provides a decision-free solution for cryo-EM, making data preprocessing more generalized and robust in the high-throughput era as well as more convenient for users from a range of backgrounds.
DepositionFeb 28, 2020-
Header (metadata) releaseMar 11, 2020-
Map releaseMar 11, 2020-
UpdateJul 22, 2020-
Current statusJul 22, 2020Processing site: RCSB / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0346
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0346
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_21492.map.gz / Format: CCP4 / Size: 41.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 222 pix.
= 270.84 Å
1.22 Å/pix.
x 222 pix.
= 270.84 Å
1.22 Å/pix.
x 222 pix.
= 270.84 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.22 Å
Contour LevelBy AUTHOR: 0.0346 / Movie #1: 0.0346
Minimum - Maximum-0.12054832 - 0.26648912
Average (Standard dev.)-0.0000379410 (±0.005837753)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 270.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.221.221.22
M x/y/z222222222
origin x/y/z0.0000.0000.000
length x/y/z270.840270.840270.840
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.1210.266-0.000

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)

Experimental details

Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen Name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 44.13 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 / Applied Symmetry: D2 (2x2 fold dihedral) / Number of Projections: 425087
3D reconstructionResolution: 3.2 Å / Resolution Method: FSC 0.143 CUT-OFF

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