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- EMDB-43287: Membrane-associated 70S ribosome in complex with SecDF -

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Basic information

Entry
Database: EMDB / ID: EMD-43287
TitleMembrane-associated 70S ribosome in complex with SecDF
Map data
Sample
  • Complex: Membrane-associated 70S ribosome in complex with SecDF
Keywordscomplex / membrane / translocation / RIBOSOME
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 26.0 Å
AuthorsPowell BM / Davis JH
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2046778 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM144542 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32-GM007287 United States
CitationJournal: bioRxiv / Year: 2023
Title: Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN.
Authors: Barrett M Powell / Joseph H Davis /
Abstract: Cryo-electron tomography (cryo-ET) allows one to observe macromolecular complexes in their native, spatially contextualized environment. Tools to visualize such complexes at nanometer resolution via ...Cryo-electron tomography (cryo-ET) allows one to observe macromolecular complexes in their native, spatially contextualized environment. Tools to visualize such complexes at nanometer resolution via iterative alignment and averaging are well-developed but rely on assumptions of structural homogeneity among the complexes under consideration. Recently developed downstream analysis tools allow for some assessment of macromolecular diversity but have limited capacity to represent highly heterogeneous macromolecules, including those undergoing continuous conformational changes. Here, we extend the highly expressive cryoDRGN deep learning architecture, originally created for cryo-electron microscopy single particle analysis, to sub-tomograms. Our new tool, tomoDRGN, learns a continuous low-dimensional representation of structural heterogeneity in cryo-ET datasets while also learning to reconstruct a large, heterogeneous ensemble of structures supported by the underlying data. Using simulated and experimental data, we describe and benchmark architectural choices within tomoDRGN that are uniquely necessitated and enabled by cryo-ET data. We additionally illustrate tomoDRGN's efficacy in analyzing an exemplar dataset, using it to reveal extensive structural heterogeneity among ribosomes imaged .
History
DepositionJan 7, 2024-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43287.png

Downloads & links

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Map

FileDownload / File: emd_43287.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
4 Å/pix.
x 192 pix.
= 768. Å		4 Å/pix.
x 192 pix.
= 768. Å		4 Å/pix.
x 192 pix.
= 768. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-0.69886476 - 2.171846
Average (Standard dev.)0.032581035 (±0.17952299)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 768.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43287_half_map_1.map
Projections & Slices
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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_43287_half_map_2.map
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Sample components

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Entire : Membrane-associated 70S ribosome in complex with SecDF

EntireName: Membrane-associated 70S ribosome in complex with SecDF
Components
  • Complex: Membrane-associated 70S ribosome in complex with SecDF

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Supramolecule #1: Membrane-associated 70S ribosome in complex with SecDF

SupramoleculeName: Membrane-associated 70S ribosome in complex with SecDF
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.93 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 380
ExtractionNumber tomograms: 65 / Number images used: 29245
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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