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- EMDB-44928: M2A Midnolin Proteasome (translocating, focused on PSMD2) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-44928
TitleM2A Midnolin Proteasome (translocating, focused on PSMD2)
Map datasharpened map (focused on PSMD2 and midnolin C-terminal helix)
Sample
  • Complex: 26 proteasome with midnolin
Keywordsproteasome / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGao J / Yip MCJ / Shao S
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01073277 United States
David and Lucile Packard Foundation2019-69660 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Structural basis for nuclear protein degradation by the midnolin-proteasome pathway
Authors: Nardone C / Gu X / Gao J / Yip MCJ / Seo H / Song K / Sebastian L / Dhe-Paganon S / Negasi M / Kamitaki N / Greenberg ME / Elledge SJ / Shao S
History
DepositionMay 19, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44928.png

Downloads & links

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Map

FileDownload / File: emd_44928.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map (focused on PSMD2 and midnolin C-terminal helix)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 363. Å		0.83 Å/pix.
x 440 pix.
= 363. Å		0.83 Å/pix.
x 440 pix.
= 363. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-2.593364 - 3.9708874
Average (Standard dev.)0.0016034674 (±0.07769423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 363.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map (focused on PSMD2 and midnolin C-terminal helix)

Fileemd_44928_additional_1.map
Annotationunsharpened map (focused on PSMD2 and midnolin C-terminal helix)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1 (focused on PSMD2 and midnolin C-terminal helix)

Fileemd_44928_half_map_1.map
Annotationhalf map 1 (focused on PSMD2 and midnolin C-terminal helix)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2 (focused on PSMD2 and midnolin C-terminal helix)

Fileemd_44928_half_map_2.map
Annotationhalf map 2 (focused on PSMD2 and midnolin C-terminal helix)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 26 proteasome with midnolin

EntireName: 26 proteasome with midnolin
Components
  • Complex: 26 proteasome with midnolin

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Supramolecule #1: 26 proteasome with midnolin

SupramoleculeName: 26 proteasome with midnolin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#41
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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 186489
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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