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- EMDB-31730: 20S proteasome (after post-processing) -

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Basic information

Entry
Database: EMDB / ID: EMD-31730
Title20S proteasome (after post-processing)
Map data
Sample
  • Complex: 20S proteasome incubated with monoUb CyclinB1-NT
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsXu C / Cong Y
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation Israel
CitationJournal: Nat Commun / Year: 2021
Title: The 20S as a stand-alone proteasome in cells can degrade the ubiquitin tag.
Authors: Indrajit Sahu / Sachitanand M Mali / Prasad Sulkshane / Cong Xu / Andrey Rozenberg / Roni Morag / Manisha Priyadarsini Sahoo / Sumeet K Singh / Zhanyu Ding / Yifan Wang / Sharleen Day / Yao ...Authors: Indrajit Sahu / Sachitanand M Mali / Prasad Sulkshane / Cong Xu / Andrey Rozenberg / Roni Morag / Manisha Priyadarsini Sahoo / Sumeet K Singh / Zhanyu Ding / Yifan Wang / Sharleen Day / Yao Cong / Oded Kleifeld / Ashraf Brik / Michael H Glickman /
Abstract: The proteasome, the primary protease for ubiquitin-dependent proteolysis in eukaryotes, is usually found as a mixture of 30S, 26S, and 20S complexes. These complexes have common catalytic sites, ...The proteasome, the primary protease for ubiquitin-dependent proteolysis in eukaryotes, is usually found as a mixture of 30S, 26S, and 20S complexes. These complexes have common catalytic sites, which makes it challenging to determine their distinctive roles in intracellular proteolysis. Here, we chemically synthesize a panel of homogenous ubiquitinated proteins, and use them to compare 20S and 26S proteasomes with respect to substrate selection and peptide-product generation. We show that 20S proteasomes can degrade the ubiquitin tag along with the conjugated substrate. Ubiquitin remnants on branched peptide products identified by LC-MS/MS, and flexibility in the 20S gate observed by cryo-EM, reflect the ability of the 20S proteasome to proteolyze an isopeptide-linked ubiquitin-conjugate. Peptidomics identifies proteasome-trapped ubiquitin-derived peptides and peptides of potential 20S substrates in Hi20S cells, hypoxic cells, and human failing-heart. Moreover, elevated levels of 20S proteasomes appear to contribute to cell survival under stress associated with damaged proteins.
History
DepositionAug 17, 2021-
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0272
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0272
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31730.png

Downloads & links

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Map

FileDownload / File: emd_31730.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 220 pix.
= 289.96 Å		1.32 Å/pix.
x 220 pix.
= 289.96 Å		1.32 Å/pix.
x 220 pix.
= 289.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.318 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0272 / Movie #1: 0.0272
Minimum - Maximum-0.101550214 - 0.17550486
Average (Standard dev.)0.00047838385 (±0.0069361157)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 289.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3181.3181.318
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z289.960289.960289.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.1020.1760.000

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Supplemental data

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Sample components

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Entire : 20S proteasome incubated with monoUb CyclinB1-NT

EntireName: 20S proteasome incubated with monoUb CyclinB1-NT
Components
  • Complex: 20S proteasome incubated with monoUb CyclinB1-NT

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Supramolecule #1: 20S proteasome incubated with monoUb CyclinB1-NT

SupramoleculeName: 20S proteasome incubated with monoUb CyclinB1-NT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
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: 7.4
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: 38.0 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154436
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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