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- EMDB-24130: Exploration of subtle structural variability of ribosome assembly... -

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Basic information

Entry
Database: EMDB / ID: EMD-24130
TitleExploration of subtle structural variability of ribosome assembly intermediates
Map dataExploration of subtle structural variability of ribosome assembly intermediates.
Sample
  • Complex: bL17-depleted large ribosomal subunit assembly intermediate
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsChen M / Ludtke SJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139 United States
CitationJournal: Nat Methods / Year: 2021
Title: Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM.
Authors: Muyuan Chen / Steven J Ludtke /
Abstract: Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. Cryogenic electron microscopy (cryo-EM) provides direct visualization of individual ...Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. Cryogenic electron microscopy (cryo-EM) provides direct visualization of individual macromolecules sampling different conformational and compositional states. While numerous methods are available for computational classification of discrete states, characterization of continuous conformational changes or large numbers of discrete state without human supervision remains challenging. Here we present e2gmm, a machine learning algorithm to determine a conformational landscape for proteins or complexes using a three-dimensional Gaussian mixture model mapped onto two-dimensional particle images in known orientations. Using a deep neural network architecture, e2gmm can automatically resolve the structural heterogeneity within the protein complex and map particles onto a small latent space describing conformational and compositional changes. This system presents a more intuitive and flexible representation than other manifold methods currently in use. We demonstrate this method on both simulated data and three biological systems to explore compositional and conformational changes at a range of scales. The software is distributed as part of EMAN2.
History
DepositionMay 28, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateSep 1, 2021-
Current statusSep 1, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24130.png

Downloads & links

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Map

FileDownload / File: emd_24130.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExploration of subtle structural variability of ribosome assembly intermediates.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.62 Å/pix.
x 128 pix.
= 335.36 Å		2.62 Å/pix.
x 128 pix.
= 335.36 Å		2.62 Å/pix.
x 128 pix.
= 335.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-8.449677 - 13.099527
Average (Standard dev.)3.3217404e-09 (±0.9999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 335.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.622.622.62
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z335.360335.360335.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-8.45013.1000.000

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Supplemental data

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Additional map: Exploration of subtle structural variability of ribosome assembly...

Fileemd_24130_additional_1.map
AnnotationExploration of subtle structural variability of ribosome assembly intermediates. Class 2.
Projections & Slices
AxesZYX

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Additional map: Exploration of subtle structural variability of ribosome assembly...

Fileemd_24130_additional_2.map
AnnotationExploration of subtle structural variability of ribosome assembly intermediates. Class 1.
Projections & Slices
AxesZYX

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Additional map: Exploration of subtle structural variability of ribosome assembly...

Fileemd_24130_additional_3.map
AnnotationExploration of subtle structural variability of ribosome assembly intermediates. Class 0.
Projections & Slices
AxesZYX

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Additional map: Exploration of subtle structural variability of ribosome assembly...

Fileemd_24130_additional_4.map
AnnotationExploration of subtle structural variability of ribosome assembly intermediates. Class 5.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Exploration of subtle structural variability of ribosome assembly...

Fileemd_24130_additional_5.map
AnnotationExploration of subtle structural variability of ribosome assembly intermediates. Class 4.
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Exploration of subtle structural variability of ribosome assembly...

Fileemd_24130_additional_6.map
AnnotationExploration of subtle structural variability of ribosome assembly intermediates. Class 3.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : bL17-depleted large ribosomal subunit assembly intermediate

EntireName: bL17-depleted large ribosomal subunit assembly intermediate
Components
  • Complex: bL17-depleted large ribosomal subunit assembly intermediate

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Supramolecule #1: bL17-depleted large ribosomal subunit assembly intermediate

SupramoleculeName: bL17-depleted large ribosomal subunit assembly intermediate
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 34.0 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

Startup modelType of model: EMDB MAP
EMDB ID:

8452

Final reconstructionNumber classes used: 6 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: OTHER
Details: 2000 particles are included in each class. The maps are filtered to 8A for visualization.
Number images used: 2000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 2.91)

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