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- EMDB-2824: Semi-automated selection of cryo-EM particles in RELION-1.3 -

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Basic information

Entry
Database: EMDB / ID: EMD-2824
TitleSemi-automated selection of cryo-EM particles in RELION-1.3
Map dataReconstruction with semi-automatically selected particles.
Sample
  • Sample: beta-galactosidase
  • Protein or peptide: beta-galactosidase
Keywordssingle-particle analysis / automated particle picking / beta-galactosidase
Function / homology
Function and homology information


alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding
Similarity search - Function
Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / : / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site ...Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / : / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsScheres SHW
CitationJournal: J Struct Biol / Year: 2015
Title: Semi-automated selection of cryo-EM particles in RELION-1.3.
Authors: Sjors H W Scheres /
Abstract: The selection of particles suitable for high-resolution cryo-EM structure determination from noisy micrographs may represent a tedious and time-consuming step. Here, a semi-automated particle ...The selection of particles suitable for high-resolution cryo-EM structure determination from noisy micrographs may represent a tedious and time-consuming step. Here, a semi-automated particle selection procedure is presented that has been implemented within the open-source software RELION. At the heart of the procedure lies a fully CTF-corrected template-based picking algorithm, which is supplemented by a fast sorting algorithm and reference-free 2D class averaging to remove false positives. With only limited user-interaction, the proposed procedure yields results that are comparable to manual particle selection. Together with an improved graphical user interface, these developments further contribute to turning RELION from a stand-alone refinement program into a convenient image processing pipeline for the entire single-particle approach.
History
DepositionNov 19, 2014-
Header (metadata) releaseDec 10, 2014-
Map releaseDec 10, 2014-
UpdateMar 11, 2015-
Current statusMar 11, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-2824.tif

Downloads & links

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Map

FileDownload / File: emd_2824.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction with semi-automatically selected particles.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 180 pix.
= 318.6 Å		1.77 Å/pix.
x 180 pix.
= 318.6 Å		1.77 Å/pix.
x 180 pix.
= 318.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.41184917 - 0.74745452
Average (Standard dev.)0.00064884 (±0.03866324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 318.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z318.600318.600318.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.4120.7470.001

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Supplemental data

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Sample components

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Entire : beta-galactosidase

EntireName: beta-galactosidase
Components
  • Sample: beta-galactosidase
  • Protein or peptide: beta-galactosidase

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Supramolecule #1000: beta-galactosidase

SupramoleculeName: beta-galactosidase / type: sample / ID: 1000 / Oligomeric state: hometetramer / Number unique components: 1
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: beta-galactosidase

MacromoleculeName: beta-galactosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: No
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 465 KDa
SequenceUniProtKB: Beta-galactosidase / GO: beta-galactosidase activity

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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

Concentration1 mg/mL
GridDetails: glow-discharged Quantifoil grids
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: manual blotting

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Electron microscopy

MicroscopeFEI POLARA 300
DateJun 12, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 84 / Average electron dose: 24 e/Å2
Details: Every image is the average of 24 raw (unaligned) movie frames. The complete set of electron micrographs used to obtain the density map presented here is available through the Electron ...Details: Every image is the average of 24 raw (unaligned) movie frames. The complete set of electron micrographs used to obtain the density map presented here is available through the Electron Microscopy Pilot Image ARchive (EMPIAR).
Tilt angle min0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 79096 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.962 µm / Nominal defocus min: 1.359 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using the new semi-automatic particle selection procedures in RELION-1.3. This reconstruction was done to test these procedures.
CTF correctionDetails: RELION
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: OTHER / Software - Name: RELION, CTFFIND3 / Number images used: 42755
Final angle assignmentDetails: RELION
FSC plot (resolution estimation)

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