5YR0 | pdb_00005yr0

Structure of Beclin1-UVRAG coiled coil domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.195 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5YR0

This is version 1.3 of the entry. See complete history

Literature

Targeting the potent Beclin 1-UVRAG coiled-coil interaction with designed peptides enhances autophagy and endolysosomal trafficking.

Wu, S.He, Y.Qiu, X.Yang, W.Liu, W.Li, X.Li, Y.Shen, H.M.Wang, R.Yue, Z.Zhao, Y.

(2018) Proc Natl Acad Sci U S A 115: E5669-E5678

  • DOI: https://doi.org/10.1073/pnas.1721173115
  • Primary Citation Related Structures: 
    5YR0

  • PubMed Abstract: 

    The Beclin 1-Vps34 complex, known as "mammalian class III PI3K," plays essential roles in membrane-mediated transport processes including autophagy and endosomal trafficking. Beclin 1 acts as a scaffolding molecule for the complex and readily transits from its metastable homodimeric state to interact with key modulators such as Atg14L or UVRAG and form functionally distinct Atg14L/UVRAG-containing Beclin 1-Vps34 subcomplexes. The Beclin 1-Atg14L/UVRAG interaction relies critically on their coiled-coil domains, but the molecular mechanism remains poorly understood. We determined the crystal structure of Beclin 1-UVRAG coiled-coil complex and identified a strengthened interface with both hydrophobic pairings and electrostatically complementary interactions. This structure explains why the Beclin 1-UVRAG interaction is more potent than the metastable Beclin 1 homodimer. Potent Beclin 1-UVRAG interaction is functionally significant because it renders UVRAG more competitive than Atg14L in Beclin 1 binding and is critical for promoting endolysosomal trafficking. UVRAG coiled-coil mutants with weakened Beclin 1 binding do not outcompete Atg14L and fail to promote endolysosomal degradation of the EGF receptor (EGFR). We designed all-hydrocarbon stapled peptides that specifically targeted the C-terminal part of the Beclin 1 coiled-coil domain to interfere with its homodimerization. One such peptide reduced Beclin 1 self-association, promoted Beclin 1-Atg14L/UVRAG interaction, increased autophagic flux, and enhanced EGFR degradation. Our results demonstrate that the targeting Beclin 1 coiled-coil domain with designed peptides to induce the redistribution of Beclin 1 among its self-associated form or Atg14L/UVRAG-containing complexes enhances both autophagy and endolysosomal trafficking.


  • Organizational Affiliation
    • Department of Applied Biology and Chemical Technology, State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 11.59 kDa 
  • Atom Count: 999 
  • Modeled Residue Count: 92 
  • Deposited Residue Count: 98 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beclin-150Mus musculusMutation(s): 0 
Gene Names: Becn1
UniProt & NIH Common Fund Data Resources
Find proteins for O88597 (Mus musculus)
Explore O88597 
Go to UniProtKB:  O88597
IMPC:  MGI:1891828
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO88597
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
UV radiation resistance associated protein48Mus musculusMutation(s): 1 
Gene Names: UvragUvrag1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8K245 (Mus musculus)
Explore Q8K245 
Go to UniProtKB:  Q8K245
IMPC:  MGI:1925860
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8K245
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.195 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.112α = 90
b = 45.112β = 90
c = 161.524γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references