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- EMDB-19343: Human 20S core particle beta7 tagged -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-19343
TitleHuman 20S core particle beta7 tagged
Map data
Sample
  • Complex: Human 20S core particle beta7 tagged
KeywordsComplex / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsSchulman BA / Hanna JW / Harper JW / Adolf F / Du J / Rawson SD / Walsh Jr RM / Goodall EA
Funding support Germany, United States, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
Aligning Science Across Parkinsons (ASAP) United States
CitationJournal: bioRxiv / Year: 2024
Title: Visualizing chaperone-mediated multistep assembly of the human 20S proteasome.
Authors: Frank Adolf / Jiale Du / Ellen A Goodall / Richard M Walsh / Shaun Rawson / Susanne von Gronau / J Wade Harper / John Hanna / Brenda A Schulman /
Abstract: Dedicated assembly factors orchestrate stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP) that mediates protein degradation. Here, we report cryo- ...Dedicated assembly factors orchestrate stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP) that mediates protein degradation. Here, we report cryo-EM reconstructions of seven recombinant human subcomplexes that visualize all five chaperones and the three active site propeptides across a wide swath of the assembly pathway. Comparison of these chaperone-bound intermediates and a matching mature CP reveals molecular mechanisms determining the order of successive subunit additions, and how proteasome subcomplexes and assembly factors structurally adapt upon progressive subunit incorporation to stabilize intermediates, facilitate the formation of subsequent intermediates, and ultimately rearrange to coordinate proteolytic activation with gated access to active sites. The structural findings reported here explain many previous biochemical and genetic observations. This work establishes a methodologic approach for structural analysis of multiprotein complex assembly intermediates, illuminates specific functions of assembly factors, and reveals conceptual principles underlying human proteasome biogenesis.
History
DepositionJan 3, 2024-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19343.png

Downloads & links

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Map

FileDownload / File: emd_19343.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.78 Å/pix.
x 64 pix.
= 241.92 Å		3.78 Å/pix.
x 64 pix.
= 241.92 Å		3.78 Å/pix.
x 64 pix.
= 241.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.1.1811.1811.181
CCP4 map header3.783.783.78
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-0.9667583 - 1.9581693
Average (Standard dev.)0.0030504996 (±0.07466172)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 330.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19343_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19343_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human 20S core particle beta7 tagged

EntireName: Human 20S core particle beta7 tagged
Components
  • Complex: Human 20S core particle beta7 tagged

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Supramolecule #1: Human 20S core particle beta7 tagged

SupramoleculeName: Human 20S core particle beta7 tagged / 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 186363
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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