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- PDB-6hol: Structure of ATG14 LIR motif bound to GABARAPL1 -

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Basic information

Entry
Database: PDB / ID: 6hol
TitleStructure of ATG14 LIR motif bound to GABARAPL1
Components
  • Beclin 1-associated autophagy-related key regulator
  • Gamma-aminobutyric acid receptor-associated protein-like 1
KeywordsSIGNALING PROTEIN / Autophagy / ATG8 / LIR
Function / homology
Function and homology information


extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / phosphatidylinositol 3-kinase complex, class III / response to mitochondrial depolarisation / glycophagy / mitochondria-associated endoplasmic reticulum membrane contact site / regulation of protein complex stability / early endosome to late endosome transport ...extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / phosphatidylinositol 3-kinase complex, class III / response to mitochondrial depolarisation / glycophagy / mitochondria-associated endoplasmic reticulum membrane contact site / regulation of protein complex stability / early endosome to late endosome transport / phosphatidylinositol 3-kinase regulator activity / phagophore assembly site membrane / protein targeting to lysosome / GABA receptor binding / Tat protein binding / phosphatidylethanolamine binding / phagophore assembly site / phosphatidylinositol-3-phosphate biosynthetic process / cellular response to nitrogen starvation / post-transcriptional regulation of gene expression / endosome to lysosome transport / Macroautophagy / autophagosome membrane docking / negative regulation of protein phosphorylation / autophagosome membrane / axoneme / autophagosome assembly / autophagosome maturation / regulation of macroautophagy / beta-tubulin binding / cellular response to glucose starvation / mitophagy / phagocytic vesicle / protein-membrane adaptor activity / autophagosome / cytoplasmic vesicle membrane / cellular response to starvation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / phospholipid binding / positive regulation of protein phosphorylation / GTPase binding / defense response to virus / microtubule / cilium / ciliary basal body / innate immune response / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / 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
Beclin 1-associated autophagy-related key regulator / Gamma-aminobutyric acid receptor-associated protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Gamma-aminobutyric acid receptor-associated protein-like 1
B: Gamma-aminobutyric acid receptor-associated protein-like 1
C: Beclin 1-associated autophagy-related key regulator
D: Beclin 1-associated autophagy-related key regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0758
Polymers32,6954
Non-polymers3804
Water3,315184
1
A: Gamma-aminobutyric acid receptor-associated protein-like 1
C: Beclin 1-associated autophagy-related key regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4443
Polymers16,3482
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-19 kcal/mol
Surface area7220 Å2
MethodPISA
2
B: Gamma-aminobutyric acid receptor-associated protein-like 1
D: Beclin 1-associated autophagy-related key regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6325
Polymers16,3482
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-29 kcal/mol
Surface area7510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.460, 41.620, 46.240
Angle α, β, γ (deg.)86.08, 76.27, 86.70
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein-like 1 / Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular ...Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular epithelial cell protein 1 / GEC-1


Mass: 14598.667 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0R8
#2: Protein/peptide Beclin 1-associated autophagy-related key regulator / Barkor / Autophagy-related protein 14-like protein / Atg14L


Mass: 1748.867 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6ZNE5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.96 Å3/Da / Density % sol: 37.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 1M LiCl, 0.1M HEPES pH7, 20% PEG 6000

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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: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.4→41.485 Å / Num. obs: 45978 / % possible obs: 93.3 % / Redundancy: 2.4 % / Biso Wilson estimate: 15.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.06 / Rrim(I) all: 0.1 / Net I/σ(I): 6.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4496 / CC1/2: 0.46 / Rpim(I) all: 0.55 / Rrim(I) all: 0.9 / % possible all: 90.33

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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: 2R2Q

2r2q


Resolution: 1.4→41.485 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.48
RfactorNum. reflection% reflection
Rfree0.2028 2211 4.84 %
Rwork0.1637 --
obs0.1655 45709 93.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→41.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 21 184 2327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152283
X-RAY DIFFRACTIONf_angle_d1.3473113
X-RAY DIFFRACTIONf_dihedral_angle_d8.9171397
X-RAY DIFFRACTIONf_chiral_restr0.113310
X-RAY DIFFRACTIONf_plane_restr0.011412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.43050.30821500.23662590X-RAY DIFFRACTION90
1.4305-1.46380.26441100.21732661X-RAY DIFFRACTION91
1.4638-1.50040.29281380.19762684X-RAY DIFFRACTION91
1.5004-1.54090.27581310.1892650X-RAY DIFFRACTION91
1.5409-1.58630.23751410.17982658X-RAY DIFFRACTION92
1.5863-1.63750.21971570.16522685X-RAY DIFFRACTION92
1.6375-1.6960.22311370.15632652X-RAY DIFFRACTION92
1.696-1.76390.20631360.15272677X-RAY DIFFRACTION93
1.7639-1.84420.22161310.15692676X-RAY DIFFRACTION91
1.8442-1.94140.23651410.15132775X-RAY DIFFRACTION95
1.9414-2.06310.20141210.14722810X-RAY DIFFRACTION95
2.0631-2.22230.18671360.15192813X-RAY DIFFRACTION96
2.2223-2.4460.19451400.15432838X-RAY DIFFRACTION97
2.446-2.79980.25121510.17272778X-RAY DIFFRACTION96
2.7998-3.52720.18671560.17242776X-RAY DIFFRACTION96
3.5272-41.5030.1611350.15732775X-RAY DIFFRACTION95

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