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

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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: Mol Cell / Year: 2025
Title: Structural basis for the midnolin-proteasome pathway and its role in suppressing myeloma.
Authors: Christopher Nardone / Jingjing Gao / Hyuk-Soo Seo / Julian Mintseris / Lucy Ort / Matthew C J Yip / Milen Negasi / Anna K Besschetnova / Nolan Kamitaki / Steven P Gygi / Sirano Dhe-Paganon / ...Authors: Christopher Nardone / Jingjing Gao / Hyuk-Soo Seo / Julian Mintseris / Lucy Ort / Matthew C J Yip / Milen Negasi / Anna K Besschetnova / Nolan Kamitaki / Steven P Gygi / Sirano Dhe-Paganon / Nikhil C Munshi / Mariateresa Fulciniti / Michael E Greenberg / Sichen Shao / Stephen J Elledge / Xin Gu /
Abstract: The midnolin-proteasome pathway degrades many nuclear proteins without ubiquitination, but how it operates mechanistically remains unclear. Here, we present structures of the midnolin-proteasome ...The midnolin-proteasome pathway degrades many nuclear proteins without ubiquitination, but how it operates mechanistically remains unclear. Here, we present structures of the midnolin-proteasome complex, revealing how established proteasomal components are repurposed to enable a unique form of proteolysis. While the proteasomal subunit PSMD2/Rpn1 binds to ubiquitinated or ubiquitin-like (Ubl) proteins, we discover that it also interacts with the midnolin nuclear localization sequence, elucidating how midnolin's activity is confined to the nucleus. Likewise, PSMD14/Rpn11, an enzyme that normally cleaves ubiquitin chains, surprisingly functions non-enzymatically as a receptor for the midnolin Ubl domain, positioning the substrate-binding Catch domain directly above the proteasomal entry site to guide substrates into the proteasome. Moreover, we demonstrate that midnolin downregulation is critical for the survival of myeloma cells by stabilizing the transcription factor substrate IRF4. Our findings uncover the mechanisms underlying the midnolin-proteasome pathway and midnolin downregulation as a driver of multiple myeloma.
History
DepositionMay 19, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 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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