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- EMDB-49498: Locally Refined map of RP(19S) in substrate-engaged MIDN-bound 26... -

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Entry
Database: EMDB / ID: EMD-49498
TitleLocally Refined map of RP(19S) in substrate-engaged MIDN-bound 26S Proteasome, EB-MIDN state
Map data
Sample
  • Complex: Structure of MIDN-bound human 26S proteasome in substrate engaged state EB_MIDN
KeywordsUbiquitin-indepedent / proteasome / Midnolin / MIDN-bound 26S complex / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsPeddada N / Beutler B
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI125581 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA258602 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural insights into the ubiquitin-independent midnolin-proteasome pathway.
Authors: Nagesh Peddada / Xue Zhong / Yan Yin / Danielle Renee Lazaro / Jianhui Wang / Stephen Lyon / Jin Huk Choi / Xiao-Chen Bai / Eva Marie Y Moresco / Bruce Beutler /
Abstract: The protein midnolin (MIDN) augments proteasome activity in lymphocytes and dramatically facilitates the survival and proliferation of B-lymphoid malignancies. MIDN binds both to proteasomes and to ...The protein midnolin (MIDN) augments proteasome activity in lymphocytes and dramatically facilitates the survival and proliferation of B-lymphoid malignancies. MIDN binds both to proteasomes and to substrates, but the mode of interaction with the proteasome is unknown, and the mechanism by which MIDN facilitates substrate degradation in a ubiquitin-independent manner is incompletely understood. Here, we present cryoelectron microscopy (cryo-EM) structures of the substrate-engaged, MIDN-bound human proteasome in two conformational states. MIDN induces proteasome conformations similarly to ubiquitinated substrates by using its ubiquitin-like domain to bind to the deubiquitinase RPN11 (PSMD14). By simultaneously binding to RPN1 (PSMD2) with its C-terminal α-helix, MIDN positions its substrate-carrying Catch domain above the proteasome ATPase channel through which substrates are translocated before degradation. Our findings suggest that both ubiquitin-like domain and C-terminal α-helix must bind to the proteasome for MIDN to stimulate proteasome activity.
History
DepositionFeb 28, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49498.png

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Map

FileDownload / File: emd_49498.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 640 pix.
= 687.36 Å		1.07 Å/pix.
x 640 pix.
= 687.36 Å		1.07 Å/pix.
x 640 pix.
= 687.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.165
Minimum - Maximum-0.0019409435 - 1.8412712
Average (Standard dev.)0.00045643267 (±0.01562845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 687.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49498_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49498_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of MIDN-bound human 26S proteasome in substrate engaged...

EntireName: Structure of MIDN-bound human 26S proteasome in substrate engaged state EB_MIDN
Components
  • Complex: Structure of MIDN-bound human 26S proteasome in substrate engaged state EB_MIDN

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Supramolecule #1: Structure of MIDN-bound human 26S proteasome in substrate engaged...

SupramoleculeName: Structure of MIDN-bound human 26S proteasome in substrate engaged state EB_MIDN
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Source (natural)Organism: Homo sapiens (human) / Strain: HEK 293

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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: 7.6
Details: 50 mM Tris, pH 7.5, 150 mM NaCl, 20 mM KCl,5 mM MgCl2, 1 mM TECP,
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsIn Vitro Reconstituted MIDN-26S proteasome complex

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 20794 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 623000
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 232000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6mse


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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