8GT9 | pdb_00008gt9

Selective targeting of the Beclin 2-Atg14L coiled coil complex by stapled peptides promotes autophagy and endolysosomal trafficking of GPCRs

• PDB DOI: https://doi.org/10.2210/pdb8GT9/pdb

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


• Deposited: 2022-09-07 Released: 2023-07-26 
• Deposition Author(s): Qiu, X., Zhao, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.214 (Depositor) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

The potent BECN2-ATG14 coiled-coil interaction is selectively critical for endolysosomal degradation of GPRASP1/GASP1-associated GPCRs.

Qiu, X., Li, N., Yang, Q., Wu, S., Li, X., Pan, X., Yamamoto, S., Zhang, X., Zeng, J., Liao, J., He, C., Wang, R., Zhao, Y.

(2023) Autophagy 19: 2884-2898

• PubMed: 37409929 
• DOI: https://doi.org/10.1080/15548627.2023.2233872
• Primary Citation Related Structures: 
  8GT9, 8GU7


• PubMed Abstract: 
  

  AMBRA1 autophagy and beclin 1 regulator 1; ATG14 autophagy related 14; ATG5 autophagy related 5; ATG7 autophagy related 7; BECN1 beclin 1; BECN2 beclin 2; CC coiled-coil; CQ chloroquine CNR1/CB1R cannabinoid receptor 1 DAPI 4',6-diamidino-2-phenylindole; dCCD delete CCD; DRD2/D2R dopamine receptor D2 GPRASP1/GASP1 G protein-coupled receptor associated sorting protein 1 GPCR G-protein coupled receptor; ITC isothermal titration calorimetry; IP immunoprecipitation; KD knockdown; KO knockout; MAP1LC3/LC3 microtubule associated protein 1 light chain 3; NRBF2 nuclear receptor binding factor 2; OPRD1/DOR opioid receptor delta 1 PIK3C3/VPS34 phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4/VPS15 phosphoinositide-3-kinase regulatory subunit 4; PtdIns3K class III phosphatidylinositol 3-kinase; PtdIns3P phosphatidylinositol-3-phosphate; RUBCN rubicon autophagy regulator; SQSTM1/p62 sequestosome 1; UVRAG UV radiation resistance associated; VPS vacuolar protein sorting; WT wild type.

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Organizational Affiliation: 
• Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, P. R. China.
Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, the First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, P.R. China.
The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, P.R. China.
State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, P.R. China.
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Department of Research and Development, Shenzhen Shiningbiotek Co. Ltd, Shenzhen, P. R. China.
Shenzhen Pengcheng Biopharm Co. Ltd, Shenzhen, P.R. China.
Department of Cell and Molecular Biology, Feingberg School of Medicine, Northwestern University, Chicago, IL, USA.
Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.88 kDa 
• Atom Count: 3,071 
• Modeled Residue Count: 360 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beclin-2	A, B, C, D	96	Homo sapiens	Mutation(s): 1  Gene Names: BECN2, BECN1L1, BECN1P1
UniProt & NIH Common Fund Data Resources
Find proteins for A8MW95 (Homo sapiens) Explore A8MW95  Go to UniProtKB:  A8MW95
GTEx:  ENSG00000196289

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.214 (Depositor) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.23	α = 90
b = 142.78	β = 90
c = 140.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEIT	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Qiu, X., Zhao, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32000864

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references