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- PDB-6hoj: Structure of Beclin1 LIR motif bound to GABARAP -

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Basic information

Entry
Database: PDB / ID: 6hoj
TitleStructure of Beclin1 LIR 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 / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of protein K48-linked ubiquitination / 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 / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of protein K48-linked ubiquitination / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / regulation of Rac protein signal transduction / negative regulation of lysosome organization / engulfment of apoptotic cell / positive regulation of autophagosome assembly / early endosome to late endosome transport / negative regulation of autophagosome assembly / cytoplasmic side of mitochondrial outer membrane / receptor catabolic process / protein targeting to lysosome / SMAD protein signal transduction / late endosome to vacuole transport / GABA receptor binding / phosphatidylethanolamine binding / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / phosphatidylinositol-3-phosphate biosynthetic process / TBC/RABGAPs / cellular response to nitrogen starvation / negative regulation of programmed cell death / microtubule associated complex / lysosome organization / response to iron(II) ion / mitotic metaphase chromosome alignment / response to vitamin E / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / Macroautophagy / RSV-host interactions / p38MAPK cascade / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / autophagosome membrane / extrinsic apoptotic signaling pathway via death domain receptors / axoneme / autophagosome assembly / autophagosome maturation / amyloid-beta metabolic process / regulation of macroautophagy / beta-tubulin binding / neuron development / cellular defense response / protein targeting / smooth endoplasmic reticulum / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / mitophagy / positive regulation of intrinsic apoptotic signaling pathway / cellular response to copper ion / phagocytic vesicle / sperm midpiece / JNK cascade / positive regulation of autophagy / autophagosome / cellular response to amino acid starvation / cellular response to epidermal growth factor stimulus / regulation of cytokinesis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / trans-Golgi network / ISG15 antiviral mechanism / response to lead ion / GABA-ergic synapse / autophagy / microtubule cytoskeleton organization / circadian rhythm / cellular response to hydrogen peroxide / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / GTPase binding / Translation of Replicase and Assembly of the Replication Transcription Complex / protein-containing complex assembly / cytoplasmic vesicle / protein-macromolecule adaptor activity / microtubule binding / molecular adaptor activity / defense response to virus / chemical synaptic transmission / microtubule / response to hypoxia / lysosome / endosome membrane / Ub-specific processing proteases / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome / regulation of autophagy / nuclear body / response to xenobiotic stimulus / Golgi membrane / negative regulation of cell population proliferation / cell division / intracellular membrane-bounded organelle
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 / Resolution: 1.51 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 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Beclin-1,Gamma-aminobutyric acid receptor-associated protein
C: Beclin-1,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7385
Polymers44,5803
Non-polymers1582
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-49 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.670, 150.490, 35.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 14859.927 Da / Num. of mol.: 3
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 4000, 50 mM Bicine pH 8.8

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.51→53.703 Å / Num. obs: 65391 / % possible obs: 99.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 21.2 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.03 / Rrim(I) all: 0.07 / Net I/σ(I): 13.2
Reflection shellResolution: 1.51→1.56 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6405 / CC1/2: 0.58 / Rpim(I) all: 0.57 / Rrim(I) all: 1.18 / % possible all: 98.89

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementResolution: 1.51→53.703 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 3254 4.98 %
Rwork0.1685 --
obs0.1706 65386 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→53.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 9 356 3373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133215
X-RAY DIFFRACTIONf_angle_d1.2214363
X-RAY DIFFRACTIONf_dihedral_angle_d20.0541959
X-RAY DIFFRACTIONf_chiral_restr0.098461
X-RAY DIFFRACTIONf_plane_restr0.008566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.53260.33381310.29272657X-RAY DIFFRACTION99
1.5326-1.55650.2581400.25772632X-RAY DIFFRACTION99
1.5565-1.5820.30561400.21822639X-RAY DIFFRACTION99
1.582-1.60930.26821490.20432698X-RAY DIFFRACTION100
1.6093-1.63860.25681410.19342646X-RAY DIFFRACTION100
1.6386-1.67010.25191210.22042670X-RAY DIFFRACTION100
1.6701-1.70420.27441470.21992687X-RAY DIFFRACTION100
1.7042-1.74120.27911390.2032651X-RAY DIFFRACTION99
1.7412-1.78170.25581350.18952701X-RAY DIFFRACTION100
1.7817-1.82630.21741390.16062660X-RAY DIFFRACTION100
1.8263-1.87570.21831370.14712729X-RAY DIFFRACTION100
1.8757-1.93090.21161550.14312631X-RAY DIFFRACTION100
1.9309-1.99320.17591580.14592683X-RAY DIFFRACTION100
1.9932-2.06450.18981430.14812688X-RAY DIFFRACTION100
2.0645-2.14710.21471380.14722695X-RAY DIFFRACTION100
2.1471-2.24480.24811350.14672728X-RAY DIFFRACTION100
2.2448-2.36320.20011240.14992737X-RAY DIFFRACTION100
2.3632-2.51120.18641340.16132710X-RAY DIFFRACTION100
2.5112-2.70510.21491370.17722726X-RAY DIFFRACTION100
2.7051-2.97730.24161590.18722750X-RAY DIFFRACTION99
2.9773-3.40810.20161370.17312721X-RAY DIFFRACTION99
3.4081-4.29360.18291440.15032779X-RAY DIFFRACTION99
4.2936-53.73690.19731710.17312914X-RAY DIFFRACTION99

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