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- PDB-8gu7: Selective targeting of the Beclin 2-Atg14L coiled coil complex by... -

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Basic information

Entry
Database: PDB / ID: 8gu7
TitleSelective targeting of the Beclin 2-Atg14L coiled coil complex by stapled peptides promotes autophagy and endolysosomal trafficking of GPCRs
Components
  • Beclin 1-associated autophagy-related key regulator
  • Beclin-2
KeywordsSTRUCTURAL PROTEIN / PI3KC3 complex / Beclin 2 / Autophagy
Function / homology
Function and homology information


G protein-coupled receptor catabolic process / extrinsic component of omegasome membrane / : / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / Macroautophagy / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / mitochondria-associated endoplasmic reticulum membrane contact site ...G protein-coupled receptor catabolic process / extrinsic component of omegasome membrane / : / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / Macroautophagy / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / mitochondria-associated endoplasmic reticulum membrane contact site / response to mitochondrial depolarisation / phagophore assembly site membrane / protein targeting to lysosome / early endosome to late endosome transport / late endosome to vacuole transport / cellular response to nitrogen starvation / phagophore assembly site / phosphatidylinositol-3-phosphate biosynthetic process / post-transcriptional regulation of gene expression / autophagosome membrane docking / endosome to lysosome transport / axoneme / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / autophagosome / regulation of macroautophagy / cellular response to glucose starvation / phosphatidylinositol 3-kinase binding / phagocytic vesicle / cellular response to starvation / negative regulation of protein phosphorylation / macroautophagy / regulation of protein phosphorylation / autophagy / GTPase binding / protein-macromolecule adaptor activity / positive regulation of protein phosphorylation / protein phosphorylation / endoplasmic reticulum membrane / cytosol
Similarity search - Function
UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region
Similarity search - Domain/homology
Beclin-2 / Beclin 1-associated autophagy-related key regulator
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsQiu, X. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000864 China
CitationJournal: Autophagy / Year: 2023
Title: The potent BECN2-ATG14 coiled-coil interaction is selectively critical for endolysosomal degradation of GPRASP1/GASP1-associated GPCRs.
Authors: 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.
History
DepositionSep 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beclin 1-associated autophagy-related key regulator
B: Beclin 1-associated autophagy-related key regulator
C: Beclin-2
D: Beclin-2


Theoretical massNumber of molelcules
Total (without water)35,9844
Polymers35,9844
Non-polymers00
Water1086
1
A: Beclin 1-associated autophagy-related key regulator
D: Beclin-2


Theoretical massNumber of molelcules
Total (without water)17,9922
Polymers17,9922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-16 kcal/mol
Surface area5390 Å2
MethodPISA
2
B: Beclin 1-associated autophagy-related key regulator
C: Beclin-2


Theoretical massNumber of molelcules
Total (without water)17,9922
Polymers17,9922
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-17 kcal/mol
Surface area5450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.500, 72.500, 68.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Beclin 1-associated autophagy-related key regulator / Barkor / Autophagy-related protein 14-like protein / Atg14L


Mass: 7021.218 Da / Num. of mol.: 2 / Mutation: C22L,C34S,G36L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Atg14, Atg14L, D14Ertd436e, Kiaa0831 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CDJ3
#2: Protein Beclin-2 / Beclin-1 autophagy-related pseudogene 1 / Beclin-1-like protein 1


Mass: 10970.921 Da / Num. of mol.: 2 / Mutation: R243L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BECN2, BECN1L1, BECN1P1 / Production host: Escherichia coli (E. coli) / References: UniProt: A8MW95
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.8 M Ammonium citrate tribasic, pH 7.0

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Data collection

DiffractionMean temperature: 289 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→51.26 Å / Num. obs: 6736 / % possible obs: 99.8 % / Redundancy: 12.2 % / CC1/2: 0.995 / Net I/σ(I): 14.1
Reflection shellResolution: 2.5→2.64 Å / Num. unique obs: 951 / CC1/2: 0.972 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
SCALEITdata reduction
SCALAdata scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GT9

8gt9


Resolution: 2.6→41.11 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.909 / SU B: 0.012 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 280 4.7 %RANDOM
Rwork0.2174 ---
obs0.2183 5705 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 172.69 Å2 / Biso mean: 66.999 Å2 / Biso min: 33.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2---0.83 Å20 Å2
3---1.66 Å2
Refinement stepCycle: final / Resolution: 2.6→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 0 6 1099
Biso mean---59.6 -
Num. residues----132
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 16 -
Rwork0.189 410 -
all-426 -
obs--100 %

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