6DCO

Bcl-xL complex with Beclin 1 BH3 domain T108D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.198 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into BCL2 pro-survival protein interactions with the key autophagy regulator BECN1 following phosphorylation by STK4/MST1.

Lee, E.F.Smith, N.A.Soares da Costa, T.P.Meftahi, N.Yao, S.Harris, T.J.Tran, S.Pettikiriarachchi, A.Perugini, M.A.Keizer, D.W.Evangelista, M.Smith, B.J.Fairlie, W.D.

(2019) Autophagy 15: 785-795

  • DOI: 10.1080/15548627.2018.1564557
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • BECN1/Beclin 1 is a critical protein in the initiation of autophagosome formation. Recent studies have shown that phosphorylation of BECN1 by STK4/MST1 at threonine 108 (T108) within its BH3 domain blocks macroautophagy/autophagy by increasing BECN1 ...

    BECN1/Beclin 1 is a critical protein in the initiation of autophagosome formation. Recent studies have shown that phosphorylation of BECN1 by STK4/MST1 at threonine 108 (T108) within its BH3 domain blocks macroautophagy/autophagy by increasing BECN1 affinity for its negative regulators, the anti-apoptotic proteins BCL2/Bcl-2 and BCL2L1/Bcl-x L . It was proposed that this increased binding is due to formation of an electrostatic interaction with a conserved histidine residue on the anti-apoptotic molecules. Here, we performed biophysical studies which demonstrated that a peptide corresponding to the BECN1 BH3 domain in which T108 is phosphorylated (p-T108) does show increased affinity for anti-apoptotic proteins that is significant, though only minor (<2-fold). We also determined X-ray crystal structures of BCL2 and BCL2L1 with T108-modified BECN1 BH3 peptides, but only showed evidence of an interaction between the BH3 peptide and the conserved histidine residue when the histidine flexibility was restrained due to crystal contacts. These data, together with molecular dynamics studies, indicate that the histidine is highly flexible, even when complexed with BECN1 BH3. Binding studies also showed that detergent can increase the affinity of the interaction. Although this increase was similar for both the phosphorylated and non-phosphorylated peptides, it suggests factors such as membranes could impact on the interaction between BECN1 and BCL2 proteins, and therefore, on the regulation of autophagy. Hence, we propose that phosphorylation of BECN1 by STK4/MST1 can increase the affinity of the interaction between BECN1 and anti-apoptotic proteins and this interaction can be stabilized by local environmental factors. Abbreviations: asu: asymmetric unit; BH3: BCL2/Bcl-2 homology 3; DAPK: death associated protein kinase; MD: molecular dynamics; MST: microscale thermophoresis; NMR: nuclear magnetic resonance; PDB: protein data bank; p-T: phosphothreonine; SPR: surface plasmon resonance; STK4/MST1: serine/threonine kinase 4.


    Organizational Affiliation

    c School of Cancer Medicine , La Trobe University , Melbourne , Australia.,b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia.,d Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , Australia.,e Structural Biology Division , The Walter and Eliza Hall Institute of Medical Research , Parkville , Australia.,a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bcl-2-like protein 1,Bcl-2-like protein 1
A, B
156Homo sapiensMutation(s): 0 
Gene Names: BCL2L1 (BCL2L, BCLX)
Find proteins for Q07817 (Homo sapiens)
Go to Gene View: BCL2L1
Go to UniProtKB:  Q07817
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beclin-1
C, D
26Homo sapiensMutation(s): 1 
Gene Names: BECN1 (GT197)
Find proteins for Q14457 (Homo sapiens)
Go to Gene View: BECN1
Go to UniProtKB:  Q14457
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.198 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 109.386α = 90.00
b = 109.386β = 90.00
c = 96.963γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)Australia1049949
Australian Research CouncilAustraliaFT150100212

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2019-01-23
    Type: Data collection, Database references
  • Version 1.2: 2019-04-17
    Type: Data collection, Database references