5K7B

Beclin 2 CCD homodimer

  • Classification: APOPTOSIS
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2016-05-25 Released: 2017-03-08 
  • Deposition Author(s): Su, M., Sinha, S.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Science Foundation (NSF, United States), North Dakota EPSCoR Track 1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

BECN2 interacts with ATG14 through a metastable coiled-coil to mediate autophagy.

Su, M.Li, Y.Wyborny, S.Neau, D.Chakravarthy, S.Levine, B.Colbert, C.L.Sinha, S.C.

(2017) Protein Sci 26: 972-984

  • DOI: https://doi.org/10.1002/pro.3140
  • Primary Citation of Related Structures:  
    5K7B, 5K9L

  • PubMed Abstract: 

    ATG14 binding to BECN/Beclin homologs is essential for autophagy, a critical catabolic homeostasis pathway. Here, we show that the α-helical, coiled-coil domain (CCD) of BECN2, a recently identified mammalian BECN1 paralog, forms an antiparallel, curved homodimer with seven pairs of nonideal packing interactions, while the BECN2 CCD and ATG14 CCD form a parallel, curved heterodimer stabilized by multiple, conserved polar interactions. Compared to BECN1, the BECN2 CCD forms a weaker homodimer, but binds more tightly to the ATG14 CCD. Mutation of nonideal BECN2 interface residues to more ideal pairs improves homodimer self-association and thermal stability. Unlike BECN1, all BECN2 CCD mutants bind ATG14, although more weakly than wild type. Thus, polar BECN2 CCD interface residues result in a metastable homodimer, facilitating dissociation, but enable better interactions with polar ATG14 residues stabilizing the BECN2:ATG14 heterodimer. These structure-based mechanistic differences in BECN1 and BECN2 homodimerization and heterodimerization likely dictate competitive ATG14 recruitment.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beclin-2
A, B, C, D
98Homo sapiensMutation(s): 0 
Gene Names: BECN2BECN1L1BECN1P1
UniProt & NIH Common Fund Data Resources
Find proteins for A8MW95 (Homo sapiens)
Explore A8MW95 
Go to UniProtKB:  A8MW95
GTEx:  ENSG00000196289 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8MW95
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.221 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.46α = 90
b = 44.32β = 96.77
c = 97.957γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesRO3 NS090939
National Science Foundation (NSF, United States)United StatesMCB-1413525
National Science Foundation (NSF, United States)United StatesIIA-1355466 Doctoral Dissertation Award
North Dakota EPSCoR Track 1United States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-05-10
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references