5K9L | pdb_00005k9l

Beclin 2 CCD N187L mutant homodimer

  • Classification: APOPTOSIS
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2016-06-01 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: 2.52 Å
  • R-Value Free: 
    0.278 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.239 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5K9L

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 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.

Macromolecule Content 

  • Total Structure Weight: 45.2 kDa 
  • Atom Count: 2,970 
  • Modeled Residue Count: 357 
  • Deposited Residue Count: 392 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beclin-2
A, B, C, D
98Homo sapiensMutation(s): 1 
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: 2.52 Å
  • R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.239 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.971α = 90
b = 44.709β = 130.57
c = 94.899γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

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
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: 2024-02-28
    Changes: Data collection, Database references