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- EMDB-4116: RELION-2.0 reconstruction for beta-galactosidase data in EMPIAR-10061 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-4116
TitleRELION-2.0 reconstruction for beta-galactosidase data in EMPIAR-10061
Map dataRELION postprocessed map
Sample
  • Complex: PETG-bound 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 (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsKimanius D / Forsberg BO / Scheres SHW / Lindahl E
CitationJournal: Elife / Year: 2016
Title: Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.
Authors: Dari Kimanius / Björn O Forsberg / Sjors Hw Scheres / Erik Lindahl /
Abstract: By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large ...By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.
History
DepositionSep 21, 2016-
Header (metadata) releaseOct 5, 2016-
Map releaseOct 5, 2016-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4116.png

Downloads & links

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Map

FileDownload / File: emd_4116.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRELION postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 384 pix.
= 244.608 Å		0.64 Å/pix.
x 384 pix.
= 244.608 Å		0.64 Å/pix.
x 384 pix.
= 244.608 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.637 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.07179602 - 0.12313014
Average (Standard dev.)-0.00001293341 (±0.0056375912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 244.608 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6370.6370.637
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z244.608244.608244.608
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0720.123-0.000

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Supplemental data

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Mask #1

Fileemd_4116_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 from gold-standard refinement procedure in RELION

Fileemd_4116_half_map_1.map
AnnotationHalf-map 1 from gold-standard refinement procedure in RELION
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 from gold-standard refinement procedure in RELION

Fileemd_4116_half_map_2.map
AnnotationHalf-map 2 from gold-standard refinement procedure in RELION
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PETG-bound beta-galactosidase

EntireName: PETG-bound beta-galactosidase
Components
  • Complex: PETG-bound beta-galactosidase

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Supramolecule #1: PETG-bound beta-galactosidase

SupramoleculeName: PETG-bound beta-galactosidase / type: complex / ID: 1 / Parent: 0
Details: B-factor corrected reconstruction of PETG-bound beta-galactosidase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 450 KDa

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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

BufferpH: 8
Details: 25 mM Tris, pH 8.0, 50 mM NaCl, 2 mM MgCl2, 1.0 mM TCEP
VitrificationCryogen name: ETHANE / Details: Blot for 2 seconds before plunging..
Details200 mesh Quantifoil R2/2 grids, plasma cleaned

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsParallel beam illumination
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsFinal map was obtained from 41,123 particles. D2 symmetry was applied throughout refinement. Map was corrected using a B-factor of -75 A^2
Particle selectionNumber selected: 130375
CTF correctionSoftware - Name: Gctf (ver. 0.50) / Details: RELION-based Wiener filtering
Startup modelType of model: EMDB MAP
EMDB ID:

2984

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0)
Details: Standard RELION post-processing, i.e. convolution effects of the solvent mask are corrected for using phase-randomisation.
Number images used: 108209
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) / Details: Standard RELION 3D auto-refine
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) / Details: Standard RELION 3D auto-refine
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 2.0)
Details: Selected 7 out of 8 3D classes. Also 2D classification was performed to select suitable particles.
FSC plot (resolution estimation)

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