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- EMDB-72140: HUWE1-USP7 local refinement, with focus on US7 catalytic domain -

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Basic information

Entry
Database: EMDB / ID: EMD-72140
TitleHUWE1-USP7 local refinement, with focus on US7 catalytic domain
Map dataHUWE1-USP7 local refinement, with focus on USP7 catalytic domain, unsharpened
Sample
  • Complex: HUWE1-USP7 complex
KeywordsComplex / E3-ligase-DUB / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsYatskevich S / Juszkiewicz S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Cell / Year: 2026
Title: Molecular mechanism of HUWE1-HAPSTR1-USP7-mediated ubiquitin chain amplification on nuclear proteins.
Authors: Stanislau Yatskevich / Jugal Mohapatra / Rana Mroue / Lilian Phu / Alexander Leitner / Caleigh M Azumaya / Richard Vandlen / Tommy K Cheung / Tik Hang Soong / Christopher M Rose / Alessandro ...Authors: Stanislau Yatskevich / Jugal Mohapatra / Rana Mroue / Lilian Phu / Alexander Leitner / Caleigh M Azumaya / Richard Vandlen / Tommy K Cheung / Tik Hang Soong / Christopher M Rose / Alessandro Ori / Claudio Ciferri / Szymon Juszkiewicz /
Abstract: Rapid protein turnover is essential for cellular stress adaptation. HUWE1 (HECT, UBA, and WWE domain containing 1), a large HECT-type E3 ligase, regulates many short-lived stress-responsive proteins, ...Rapid protein turnover is essential for cellular stress adaptation. HUWE1 (HECT, UBA, and WWE domain containing 1), a large HECT-type E3 ligase, regulates many short-lived stress-responsive proteins, yet the mechanisms underlying its substrate selectivity remain unclear. Here, we reveal that HUWE1 functions as a ubiquitin chain amplifier that captures pre-ubiquitinated substrates and amplifies the degradation signal by assembling long ubiquitin chains containing K11-K48 branch points, a process regulated by its partners HUWE1-associated protein stress response 1 (HAPSTR1) and USP7 (ubiquitin-specific-processing protease 7). Structural and biochemical analyses show that HAPSTR1 engages HUWE1's ubiquitin-binding motifs to drive nuclear import and modulate substrate recruitment. A cryo-EM structure of the HUWE1-USP7 complex reveals a bidirectional regulatory mechanism: HUWE1 activates USP7's catalytic activity, while USP7 modulates HUWE1 conformational states. Global proteomic analyses demonstrate that this axis drives extensive remodeling of the short-lived nuclear proteome. These findings establish the HUWE1-HAPSTR1-USP7 complex as a key ubiquitin code modifier, providing a molecular rationale for HUWE1 dysregulation in neurodevelopmental disorders and cancer.
History
DepositionAug 14, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72140.png

Downloads & links

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Map

FileDownload / File: emd_72140.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHUWE1-USP7 local refinement, with focus on USP7 catalytic domain, unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 380 pix.
= 277.78 Å		0.73 Å/pix.
x 380 pix.
= 277.78 Å		0.73 Å/pix.
x 380 pix.
= 277.78 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0153
Minimum - Maximum-0.07360165 - 0.14654951
Average (Standard dev.)0.00026506628 (±0.00331624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 277.78 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: HUWE1-USP7 local refinement, with focus on USP7 catalytic...

Fileemd_72140_additional_1.map
AnnotationHUWE1-USP7 local refinement, with focus on USP7 catalytic domain, sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HUWE1-USP7 local refinement, with focus on USP7 catalytic...

Fileemd_72140_half_map_1.map
AnnotationHUWE1-USP7 local refinement, with focus on USP7 catalytic domain, half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HUWE1-USP7 local refinement, with focus on USP7 catalytic...

Fileemd_72140_half_map_2.map
AnnotationHUWE1-USP7 local refinement, with focus on USP7 catalytic domain, half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HUWE1-USP7 complex

EntireName: HUWE1-USP7 complex
Components
  • Complex: HUWE1-USP7 complex

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Supramolecule #1: HUWE1-USP7 complex

SupramoleculeName: HUWE1-USP7 complex / type: complex / ID: 1 / Parent: 0
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 / Chamber humidity: 100 % / Chamber temperature: 298 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: 45.0 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: PDB ENTRY
PDB model - PDB ID:

7jq9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 118192
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: RELION

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