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- EMDB-73375: Global refinement map of p97Ufd1-Npl4 complex processing poly-ubi... -

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Basic information

Entry
Database: EMDB / ID: EMD-73375
TitleGlobal refinement map of p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP
Map dataGlobal refined map
Sample
  • Complex: p97-Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP
Keywordsp97 / VCP / AAA+ ATPase / TRANSLOCASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLi H / Rapoport T
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Sci Rep / Year: 2026
Title: The deubiquitinating enzyme Otu1 releases substrates from the conserved initiation complex of the Cdc48/p97 ATPase for proteasomal degradation.
Authors: Hao Li / Haipeng Guan / Tom A Rapoport /
Abstract: Many eukaryotic proteins are modified with a polyubiquitin chain and then recruited to either the Cdc48 ATPase (p97 or VCP in mammals) or the 26S proteasome by conserved cofactors. They can then ...Many eukaryotic proteins are modified with a polyubiquitin chain and then recruited to either the Cdc48 ATPase (p97 or VCP in mammals) or the 26S proteasome by conserved cofactors. They can then shuttle between the Cdc48 ATPase and the 26S proteasome before being degraded. How substrates avoid being trapped on the Cdc48 ATPase complex is incompletely understood, as they can undergo repeated cycles of translocation through the ATPase pore. Here, we show that the deubiquitinating enzyme (DUB) Otu1 (Yod1 in mammals) can break this futile cycle. Otu1 trims the ubiquitin chain of the substrate before its translocation through the Cdc48 pore is initiated, allowing transfer to the proteasome and subsequent degradation. A cryo-EM structure shows that the mammalian homolog Yod1 binds to p97 simultaneously with other Cdc48/p97 cofactors. As in the yeast system, polypeptide translocation through the ATPase pore is initiated by the unfolding of a ubiquitin molecule, suggesting that the mechanism of substrate processing is conserved in all eukaryotes.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42811-6.
History
DepositionOct 17, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73375.png

Downloads & links

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Map

FileDownload / File: emd_73375.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal refined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 330.8 Å		0.83 Å/pix.
x 400 pix.
= 330.8 Å		0.83 Å/pix.
x 400 pix.
= 330.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.60960144 - 1.3927333
Average (Standard dev.)0.00040680906 (±0.025327142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 330.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_73375_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73375_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : p97-Ufd1-Npl4 complex processing poly-ubiquitinated substrate in ...

EntireName: p97-Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP
Components
  • Complex: p97-Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP

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Supramolecule #1: p97-Ufd1-Npl4 complex processing poly-ubiquitinated substrate in ...

SupramoleculeName: p97-Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #7-#9
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 800 KDa

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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

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 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: PDB ENTRY
PDB model - PDB ID:

7lmz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 65959
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 2

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