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 9PLR | pdb_00009plr

CryoEM reconstruction of HUWE1-USP7 complex in the closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9PLR

This is version 1.1 of the entry. See complete history. 

Literature

Molecular mechanism of HUWE1-HAPSTR1-USP7-mediated ubiquitin chain amplification on nuclear proteins.

Yatskevich, S., Mohapatra, J., Mroue, R., Phu, L., Leitner, A., Azumaya, C.M., Vandlen, R., Cheung, T.K., Soong, T.H., Rose, C.M., Ori, A., Ciferri, C., Juszkiewicz, S.

(2026) Mol Cell 86: 3803-3821.e17

  • DOI: https://doi.org/10.1016/j.molcel.2026.08.016
  • Primary Citation Related Structures: 
    9PLQ, 9PLR

  • PubMed 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, 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.


  • Organizational Affiliation: 
    • Protein Sciences, Genentech, South San Francisco, CA 94080, USA.

Macromolecule Content 

  • Total Structure Weight: 610.9 kDa 
  • Atom Count: 27,348 
  • Modeled Residue Count: 3,422 
  • Deposited Residue Count: 5,476 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase HUWE14,374Homo sapiensMutation(s): 0 
Gene Names: HUWE1, KIAA0312, KIAA1578, UREB1, HSPC272
EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z6Z7 (Homo sapiens)
Explore Q7Z6Z7 
Go to UniProtKB:  Q7Z6Z7
PHAROS:  Q7Z6Z7
GTEx:  ENSG00000086758 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z6Z7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 7B [auth C]1,102Homo sapiensMutation(s): 0 
Gene Names: USP7, HAUSP
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q93009 (Homo sapiens)
Explore Q93009 
Go to UniProtKB:  Q93009
PHAROS:  Q93009
GTEx:  ENSG00000187555 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93009
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-22
    Type: Initial release
  • Version 1.1: 2026-09-30
    Changes: Data collection, Database references