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- EMDB-43285: Human heavy-chain holoferritin refined in C1 from cryo-ET data fi... -

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Basic information

Entry
Database: EMDB / ID: EMD-43285
TitleHuman heavy-chain holoferritin refined in C1 from cryo-ET data filtered by tomoDRGN
Map data
Sample
  • Complex: Heavy-chain holoferritin
Keywordsferritin / METAL BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 10.5 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_43285.png

Downloads & links

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Map

FileDownload / File: emd_43285.map.gz / Format: CCP4 / Size: 8.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.668 Å
Density
Contour LevelBy AUTHOR: 0.0012
Minimum - Maximum-0.0022375262 - 0.004289275
Average (Standard dev.)0.000016404309 (±0.00052353606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions132132132
Spacing132132132
CellA=B=C: 220.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43285_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43285_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heavy-chain holoferritin

EntireName: Heavy-chain holoferritin
Components
  • Complex: Heavy-chain holoferritin

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Supramolecule #1: Heavy-chain holoferritin

SupramoleculeName: Heavy-chain holoferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 2.3000000000000003 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: 10.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 542
ExtractionNumber tomograms: 37 / Number images used: 25900
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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