9CHT | pdb_00009cht

Human E3 ligase E6AP in complex with HPV16-E6 and p53


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of E6AP in complex with HPV16-E6 and p53 reveals a novel ordered domain important for E3 ligase activation.

Kenny, S.Iyer, S.Gabel, C.A.Tegenfeldt, N.DeMarco, A.G.Hall, M.C.Chang, L.Davisson, V.J.Pol, S.V.Das, C.

(2025) Structure 33: 504-516.e4

  • DOI: https://doi.org/10.1016/j.str.2024.12.013
  • Primary Citation of Related Structures:  
    9CHT

  • PubMed Abstract: 

    High-risk human papillomavirus E6 oncoprotein is a model system for the recognition and degradation of cellular p53 tumor suppressor protein. There remains a gap in the understanding of the ubiquitin transfer reaction, including placement of the E6AP catalytic HECT domain of the ligase concerning the p53 substrate and how E6 itself is protected from ubiquitination. We determined the cryoelectron microscopy (cryo-EM) structure of the E6AP/E6/p53 complex, related the structure to in vivo modeling of the tri-molecular complex, and identified structural interactions associated with activation of the ubiquitin ligase function. The structure reveals that the N-terminal ordered domain (NOD) in E6AP has a terminal alpha helix that mediates the interaction of the NOD with the HECT domain of E6AP and protects the HPV-E6 protein from ubiquitination. In addition, this NOD helix is required for E6AP ligase function by contributing to the affinity of the E6-E6AP association, modulating E6 substrate recognition, while displacing UbcH7.


  • Organizational Affiliation
    • Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-protein ligase E3A895Homo sapiensMutation(s): 0 
Gene Names: UBE3AE6APEPVE6APHPVE6A
EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q05086 (Homo sapiens)
Explore Q05086 
Go to UniProtKB:  Q05086
PHAROS:  Q05086
GTEx:  ENSG00000114062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05086
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin G-binding protein G/Cellular tumor antigen p53 fusion protein396Streptococcus sp. 'group GHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: spgTP53P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
PHAROS:  P04637
GTEx:  ENSG00000141510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04637
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein E6151Human papillomavirus 16Mutation(s): 0 
Gene Names: E6
UniProt
Find proteins for P03126 (Human papillomavirus type 16)
Explore P03126 
Go to UniProtKB:  P03126
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03126
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2.0
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateP30CA023168
American Heart AssociationUnited States905924/SK/2021
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM132024

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Data collection, Database references
  • Version 1.2: 2025-03-19
    Changes: Data collection, Database references