8Q0N

HACE1 in complex with RAC1 Q61L


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1.

During, J.Wolter, M.Toplak, J.J.Torres, C.Dybkov, O.Fokkens, T.J.Bohnsack, K.E.Urlaub, H.Steinchen, W.Dienemann, C.Lorenz, S.

(2024) Nat Struct Mol Biol 31: 364-377

  • DOI: https://doi.org/10.1038/s41594-023-01203-4
  • Primary Citation of Related Structures:  
    8PWL, 8Q0N

  • PubMed Abstract: 

    Ubiquitin ligases (E3s) are pivotal specificity determinants in the ubiquitin system by selecting substrates and decorating them with distinct ubiquitin signals. However, structure determination of the underlying, specific E3-substrate complexes has proven challenging owing to their transient nature. In particular, it is incompletely understood how members of the catalytic cysteine-driven class of HECT-type ligases (HECTs) position substrate proteins for modification. Here, we report a cryogenic electron microscopy (cryo-EM) structure of the full-length human HECT HACE1, along with solution-based conformational analyses by small-angle X-ray scattering and hydrogen-deuterium exchange mass spectrometry. Structure-based functional analyses in vitro and in cells reveal that the activity of HACE1 is stringently regulated by dimerization-induced autoinhibition. The inhibition occurs at the first step of the catalytic cycle and is thus substrate-independent. We use mechanism-based chemical crosslinking to reconstitute a complex of activated, monomeric HACE1 with its major substrate, RAC1, determine its structure by cryo-EM and validate the binding mode by solution-based analyses. Our findings explain how HACE1 achieves selectivity in ubiquitinating the active, GTP-loaded state of RAC1 and establish a framework for interpreting mutational alterations of the HACE1-RAC1 interplay in disease. More broadly, this work illuminates central unexplored aspects in the architecture, conformational dynamics, regulation and specificity of full-length HECTs.


  • Organizational Affiliation

    Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase HACE1A [auth B]889Homo sapiensMutation(s): 0 
Gene Names: HACE1KIAA1320
EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYU2 (Homo sapiens)
Explore Q8IYU2 
Go to UniProtKB:  Q8IYU2
PHAROS:  Q8IYU2
GTEx:  ENSG00000085382 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IYU2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related C3 botulinum toxin substrate 1B [auth C]213Homo sapiensMutation(s): 1 
Gene Names: RAC1TC25MIG5
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens)
Explore P63000 
Go to UniProtKB:  P63000
GTEx:  ENSG00000136238 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63000
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology Organization (EMBO)European UnionEMBO ALTF 439-2022
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Database references