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- PDB-6hok: Structure of Beclin1 LIR (S96E) motif bound to GABARAP -

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Basic information

Entry
Database: PDB / ID: 6hok
TitleStructure of Beclin1 LIR (S96E) motif bound to GABARAP
ComponentsBeclin-1,Gamma-aminobutyric acid receptor-associated protein
KeywordsSIGNALING PROTEIN / Autophagy / ATG8 / LIR
Function / homology
Function and homology information


cellular response to aluminum ion / positive regulation of stress granule assembly / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / positive regulation of protein K48-linked ubiquitination / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / regulation of Rac protein signal transduction ...cellular response to aluminum ion / positive regulation of stress granule assembly / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / positive regulation of protein K48-linked ubiquitination / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / regulation of Rac protein signal transduction / engulfment of apoptotic cell / negative regulation of lysosome organization / positive regulation of autophagosome assembly / cytoplasmic side of mitochondrial outer membrane / early endosome to late endosome transport / negative regulation of autophagosome assembly / receptor catabolic process / SMAD protein signal transduction / late endosome to vacuole transport / protein targeting to lysosome / GABA receptor binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / phosphatidylinositol-3-phosphate biosynthetic process / negative regulation of programmed cell death / mitotic metaphase chromosome alignment / response to vitamin E / lysosome organization / Macroautophagy / response to iron(II) ion / positive regulation of cardiac muscle hypertrophy / RSV-host interactions / cytoplasmic pattern recognition receptor signaling pathway / p38MAPK cascade / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum / autophagosome membrane / protein secretion / extrinsic apoptotic signaling pathway via death domain receptors / amyloid-beta metabolic process / regulation of macroautophagy / autophagosome maturation / cellular defense response / axoneme / neuron development / autophagosome assembly / protein targeting / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / mitophagy / beta-tubulin binding / phagocytic vesicle / JNK cascade / positive regulation of intrinsic apoptotic signaling pathway / positive regulation of autophagy / autophagosome / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / regulation of cytokinesis / regulation of autophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / trans-Golgi network / circadian rhythm / bone development / response to lead ion / GABA-ergic synapse / ISG15 antiviral mechanism / microtubule cytoskeleton organization / autophagy / cellular response to hydrogen peroxide / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / GTPase binding / protein-containing complex assembly / cytoplasmic vesicle / sperm midpiece / Translation of Replicase and Assembly of the Replication Transcription Complex / microtubule binding / defense response to virus / molecular adaptor activity / chemical synaptic transmission / microtubule / protein-macromolecule adaptor activity / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosome / endosome / endosome membrane / Ub-specific processing proteases / nuclear body / response to xenobiotic stimulus / negative regulation of cell population proliferation / Golgi membrane
Similarity search - Function
Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like ...Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / Beclin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsMouilleron, S. / Birgisdottir, A.B. / Bhujbal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S. ...Mouilleron, S. / Birgisdottir, A.B. / Bhujbal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S. / Lamark, T. / Johansen, T.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway214448 Norway
Research Council of Norway249884 Norway
CitationJournal: Autophagy / Year: 2019
Title: Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs.
Authors: Birgisdottir, A.B. / Mouilleron, S. / Bhujabal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S.A. / Lamark, T. / Johansen, T.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beclin-1,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0263
Polymers14,9021
Non-polymers1242
Water1,62190
1
A: Beclin-1,Gamma-aminobutyric acid receptor-associated protein
hetero molecules

A: Beclin-1,Gamma-aminobutyric acid receptor-associated protein
hetero molecules

A: Beclin-1,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0789
Polymers44,7063
Non-polymers3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6960 Å2
ΔGint-14 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.640, 140.640, 140.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21A-357-

HOH

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Components

#1: Protein Beclin-1,Gamma-aminobutyric acid receptor-associated protein / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197 / GABA(A) receptor-associated protein / MM46


Mass: 14901.962 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BECN1, GT197, GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14457, UniProt: O95166
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.89 Å3/Da / Density % sol: 68.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.6 M ammonium sulfate, 100 mM TRIS pH 8.5, 10 % Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.61→49.72 Å / Num. obs: 30838 / % possible obs: 99.01 % / Redundancy: 6.8 % / Biso Wilson estimate: 28.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.01 / Rrim(I) all: 0.04 / Net I/σ(I): 17.1
Reflection shellResolution: 1.61→1.66 Å / Redundancy: 7 % / Rmerge(I) obs: 1.16 / Num. unique obs: 2999 / CC1/2: 0.61 / Rpim(I) all: 0.47 / Rrim(I) all: 1.26 / % possible all: 96.84

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNU

1gnu


Resolution: 1.61→57.416 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1982 1998 6.53 %
Rwork0.1658 --
obs0.1679 30605 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→57.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 8 90 1120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011100
X-RAY DIFFRACTIONf_angle_d1.0351492
X-RAY DIFFRACTIONf_dihedral_angle_d18.404666
X-RAY DIFFRACTIONf_chiral_restr0.065156
X-RAY DIFFRACTIONf_plane_restr0.006196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6101-1.65030.42141380.37171943X-RAY DIFFRACTION96
1.6503-1.6950.39851400.33381982X-RAY DIFFRACTION97
1.695-1.74480.36131400.31591995X-RAY DIFFRACTION98
1.7448-1.80120.3591390.26792011X-RAY DIFFRACTION99
1.8012-1.86550.28221410.22232020X-RAY DIFFRACTION99
1.8655-1.94020.25251410.1782012X-RAY DIFFRACTION99
1.9402-2.02860.19651420.1362038X-RAY DIFFRACTION100
2.0286-2.13550.17481420.14492042X-RAY DIFFRACTION99
2.1355-2.26930.19671430.13552041X-RAY DIFFRACTION99
2.2693-2.44450.17951410.13942036X-RAY DIFFRACTION100
2.4445-2.69050.18331440.14552070X-RAY DIFFRACTION100
2.6905-3.07980.21221450.16752082X-RAY DIFFRACTION100
3.0798-3.88010.16841480.15882113X-RAY DIFFRACTION100
3.8801-57.45260.18081540.15852222X-RAY DIFFRACTION99

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