Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 3.78 kDa 
• Atom Count: 154 
• Residue Count: 15 
• Unique protein chains: 1

5EFM

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

• DOI: 10.2210/pdb5EFM/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Mutation(s): No 


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

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Experimental Data Snapshot

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

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

• PubMed: 26937551 
• DOI: 10.1021/acs.biochem.5b01264
• Primary Citation of Related Structures:  
  5EFM


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beclin-1	A	31	Homo sapiens	Mutation(s): 0  Gene Names: BECN1, GT197
Find proteins for Q14457 (Homo sapiens) Explore Q14457  Go to UniProtKB:  Q14457
NIH Common Fund Data Resources
PHAROS  Q14457 GTEx  ENSG00000126581

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.216 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.163	α = 90
b = 63.163	β = 90
c = 63.163	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
Coot	model building
SHELXD	phasing
XDS	data reduction
XSCALE	data scaling

Structure Validation

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
  Changes: Database references, Derived calculations, Refinement description