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- PDB-6hog: Structure of VPS34 LIR motif bound to GABARAP -

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Basic information

Entry
Database: PDB / ID: 6hog
TitleStructure of VPS34 LIR motif bound to GABARAP
ComponentsPhosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
KeywordsSIGNALING PROTEIN / Autophagy / ATG8 / LIR
Function / homology
Function and homology information


positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of protein K48-linked ubiquitination / presynaptic endosome ...positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of protein K48-linked ubiquitination / presynaptic endosome / host-mediated activation of viral genome replication / regulation of Rac protein signal transduction / phosphatidylinositol kinase activity / Synthesis of PIPs at the Golgi membrane / early endosome to late endosome transport / response to L-leucine / protein localization to phagophore assembly site / protein targeting to lysosome / endosome organization / pexophagy / GABA receptor binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / TBC/RABGAPs / phosphatidylinositol-3-phosphate biosynthetic process / cellular response to nitrogen starvation / phosphatidylinositol 3-kinase / microtubule associated complex / 1-phosphatidylinositol-3-kinase activity / Macroautophagy / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum / autolysosome / autophagosome membrane / PI3K Cascade / extrinsic apoptotic signaling pathway via death domain receptors / RHO GTPases Activate NADPH Oxidases / axoneme / synaptic vesicle endocytosis / autophagosome maturation / regulation of macroautophagy / autophagosome assembly / beta-tubulin binding / protein targeting / cellular response to glucose starvation / mitophagy / autophagosome / regulation of cytokinesis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein processing / regulation of autophagy / autophagy / GABA-ergic synapse / microtubule cytoskeleton organization / phagocytic vesicle membrane / endocytosis / peroxisome / late endosome / sperm midpiece / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / protein transport / cytoplasmic vesicle / midbody / Translation of Replicase and Assembly of the Replication Transcription Complex / microtubule binding / chemical synaptic transmission / microtubule / protein kinase activity / lysosome / endosome / intracellular membrane-bounded organelle / Golgi membrane / cell division / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / glutamatergic synapse / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Phosphatidylinositol 3-kinase, Vps34 type / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily ...Phosphatidylinositol 3-kinase, Vps34 type / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / C2 domain superfamily / Ubiquitin-like (UB roll) / Armadillo-type fold / Ubiquitin-like domain superfamily / Roll / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6927
Polymers15,1911
Non-polymers5006
Water1,47782
1
A: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
hetero molecules

A: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
hetero molecules

A: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,07621
Polymers45,5743
Non-polymers1,50118
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8100 Å2
ΔGint-110 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.100, 92.100, 41.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-201-

SO4

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Components

#1: Protein Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein / PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase ...PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase class 3 / hVps34 / GABA(A) receptor-associated protein / MM46


Mass: 15191.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C3, VPS34, GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NEB9, UniProt: O95166, phosphatidylinositol 3-kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50 mM HEPES pH 7.1, 40% PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.26→28.6 Å / Num. obs: 34959 / % possible obs: 99.17 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.01 / Rrim(I) all: 0.03 / Net I/σ(I): 19.2
Reflection shellResolution: 1.26→1.3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10172 / CC1/2: 0.53 / Rpim(I) all: 0.49 / Rrim(I) all: 0.89 / % possible all: 98.19

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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: 1.26→28.6 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.51
RfactorNum. reflection% reflection
Rfree0.1809 1581 4.52 %
Rwork0.1545 --
obs0.1556 34958 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.26→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 30 82 1117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051114
X-RAY DIFFRACTIONf_angle_d0.7931514
X-RAY DIFFRACTIONf_dihedral_angle_d24.848429
X-RAY DIFFRACTIONf_chiral_restr0.085159
X-RAY DIFFRACTIONf_plane_restr0.005196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.30070.33821170.28573048X-RAY DIFFRACTION98
1.3007-1.34720.2641340.25183007X-RAY DIFFRACTION99
1.3472-1.40110.23141500.20443033X-RAY DIFFRACTION99
1.4011-1.46490.2311560.17383008X-RAY DIFFRACTION99
1.4649-1.54210.19391770.14163012X-RAY DIFFRACTION100
1.5421-1.63870.15421390.12023049X-RAY DIFFRACTION100
1.6387-1.76530.19331470.12333060X-RAY DIFFRACTION99
1.7653-1.94290.1681460.12033024X-RAY DIFFRACTION100
1.9429-2.22390.16971470.13123049X-RAY DIFFRACTION100
2.2239-2.80150.21081250.16443076X-RAY DIFFRACTION99
2.8015-28.67240.16061430.16153011X-RAY DIFFRACTION99

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