5EFM

Beclin 1 Flexible-helical Domian (FHD) (141-171)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformational Flexibility Enables the Function of a BECN1 Region Essential for Starvation-Mediated Autophagy.

Mei, Y.Ramanathan, A.Glover, K.Stanley, C.Sanishvili, R.Chakravarthy, S.Yang, Z.Colbert, C.L.Sinha, S.C.

(2016) Biochemistry 55: 1945-1958

  • DOI: 10.1021/acs.biochem.5b01264

  • PubMed Abstract: 
  • BECN1 is essential for autophagy, a critical eukaryotic cellular homeostasis pathway. Here we delineate a highly conserved BECN1 domain located between previously characterized BH3 and coiled-coil domains and elucidate its structure and role in autop ...

    BECN1 is essential for autophagy, a critical eukaryotic cellular homeostasis pathway. Here we delineate a highly conserved BECN1 domain located between previously characterized BH3 and coiled-coil domains and elucidate its structure and role in autophagy. The 2.0 Å sulfur-single-wavelength anomalous dispersion X-ray crystal structure of this domain demonstrates that its N-terminal half is unstructured while its C-terminal half is helical; hence, we name it the flexible helical domain (FHD). Circular dichroism spectroscopy, double electron-electron resonance-electron paramagnetic resonance, and small-angle X-ray scattering (SAXS) analyses confirm that the FHD is partially disordered, even in the context of adjacent BECN1 domains. Molecular dynamic simulations fitted to SAXS data indicate that the FHD transiently samples more helical conformations. FHD helicity increases in 2,2,2-trifluoroethanol, suggesting it may become more helical upon binding. Lastly, cellular studies show that conserved FHD residues are required for starvation-induced autophagy. Thus, the FHD likely undergoes a binding-associated disorder-to-helix transition, and conserved residues critical for this interaction are essential for starvation-induced autophagy.


    Organizational Affiliation

    Health Data Sciences Institute, Computational Science and Engineering Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States.,Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58108-6050, United States.,Bio-CAT, Advanced Photon Source , 9700 South Cass Avenue, Building 435B, Argonne, Illinois 60439, United States.,GMCA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States.,Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beclin-1
A
31Homo sapiensMutation(s): 0 
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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.212 
  • Space Group: P 43 3 2
Unit Cell:
Length (Å)Angle (°)
a = 63.163α = 90.00
b = 63.163β = 90.00
c = 63.163γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
Cootmodel building
XDSdata reduction
XDSdata scaling
SHELXDphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-10-23 
  • Released Date: 2016-07-20 
  • Deposition Author(s): Sinha, S., Mei, Y.

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Database references, Derived calculations, Refinement description