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- PDB-8gt9: Selective targeting of the Beclin 2-Atg14L coiled coil complex by... -

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Basic information

Entry
Database: PDB / ID: 8gt9
TitleSelective targeting of the Beclin 2-Atg14L coiled coil complex by stapled peptides promotes autophagy and endolysosomal trafficking of GPCRs
ComponentsBeclin-2
KeywordsSTRUCTURAL PROTEIN / PI3KC3 complex / Beclin 2 / Autophagy
Function / homology
Function and homology information


G protein-coupled receptor catabolic process / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / late endosome to vacuole transport / phagophore assembly site / cellular response to nitrogen starvation / endosome to lysosome transport / autophagosome assembly / phosphatidylinositol 3-kinase binding / mitophagy ...G protein-coupled receptor catabolic process / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / late endosome to vacuole transport / phagophore assembly site / cellular response to nitrogen starvation / endosome to lysosome transport / autophagosome assembly / phosphatidylinositol 3-kinase binding / mitophagy / autophagy / glucose homeostasis / protein-macromolecule adaptor activity / protein-containing complex binding
Similarity search - Function
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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 7, 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

Downloads & links

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Assembly

Deposited unit
A: Beclin-2
B: Beclin-2
C: Beclin-2
D: Beclin-2


Theoretical massNumber of molelcules
Total (without water)43,8844
Polymers43,8844
Non-polymers00
Water2,306128
1
A: Beclin-2
B: Beclin-2


Theoretical massNumber of molelcules
Total (without water)21,9422
Polymers21,9422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-47 kcal/mol
Surface area12560 Å2
MethodPISA
2
C: Beclin-2
D: Beclin-2


Theoretical massNumber of molelcules
Total (without water)21,9422
Polymers21,9422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-42 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.230, 142.780, 140.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Beclin-2 / Beclin-1 autophagy-related pseudogene 1 / Beclin-1-like protein 1


Mass: 10970.921 Da / Num. of mol.: 4 / 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 0.1 M MES, pH6.5, and 10% Dioxane.

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Data collection

DiffractionMean temperature: 289 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.91836 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91836 Å / Relative weight: 1
ReflectionResolution: 1.9→70.39 Å / Num. obs: 34484 / % possible obs: 90.9 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.7
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.282 / Num. unique obs: 4709

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.27data extraction
SCALEITdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→70 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.104 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 1476 4.9 %RANDOM
Rwork0.2138 ---
obs0.2147 28367 91.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.36 Å2 / Biso mean: 21.302 Å2 / Biso min: 9.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---2.09 Å2-0 Å2
3---1.39 Å2
Refinement stepCycle: final / Resolution: 2→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 0 128 3044
Biso mean---24.7 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192960
X-RAY DIFFRACTIONr_bond_other_d0.0020.022696
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9683997
X-RAY DIFFRACTIONr_angle_other_deg1.0636230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3245366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75625.34206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29115549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8791540
X-RAY DIFFRACTIONr_chiral_restr0.1220.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023447
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02577
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 110 -
Rwork0.203 1937 -
all-2047 -
obs--85.11 %

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