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- PDB-6hyn: Structure of ATG13 LIR motif bound to GABARAP -

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Basic information

Entry
Database: PDB / ID: 6hyn
TitleStructure of ATG13 LIR motif bound to GABARAP
ComponentsAutophagy-related protein 13,Gamma-aminobutyric acid receptor-associated protein
KeywordsSIGNALING PROTEIN / Autophagy / ATG8 / LIR
Function / homology
Function and homology information


regulation of protein lipidation / Atg1/ULK1 kinase complex / positive regulation of protein K48-linked ubiquitination / response to mitochondrial depolarisation / regulation of Rac protein signal transduction / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / GABA receptor binding / cellular response to nitrogen starvation ...regulation of protein lipidation / Atg1/ULK1 kinase complex / positive regulation of protein K48-linked ubiquitination / response to mitochondrial depolarisation / regulation of Rac protein signal transduction / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / phagophore assembly site / TBC/RABGAPs / microtubule associated complex / positive regulation of protein targeting to mitochondrion / Macroautophagy / beta-tubulin binding / axoneme / smooth endoplasmic reticulum / autophagosome membrane / mitophagy / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome / protein targeting / positive regulation of autophagy / sperm midpiece / protein serine/threonine kinase activator activity / macroautophagy / microtubule cytoskeleton organization / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / chemical synaptic transmission / cytoplasmic vesicle / microtubule binding / microtubule / lysosome / negative regulation of cell population proliferation / Golgi membrane / synapse / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein kinase binding / mitochondrion / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / HORMA domain superfamily / 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
Autophagy-related protein 13 / Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsMouilleron, S. / Wirth, M. / Zhang, W. / O'Reilly, N. / Tooze, S. / Johansen, T. / Razi, M. / Nyoni, L. / Joshi, D.
CitationJournal: Nat Commun / Year: 2019
Title: Molecular determinants regulating selective binding of autophagy adapters and receptors to ATG8 proteins.
Authors: Wirth, M. / Zhang, W. / Razi, M. / Nyoni, L. / Joshi, D. / O'Reilly, N. / Johansen, T. / Tooze, S.A. / Mouilleron, S.
History
DepositionOct 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 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: Autophagy-related protein 13,Gamma-aminobutyric acid receptor-associated protein


Theoretical massNumber of molelcules
Total (without water)16,1831
Polymers16,1831
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.131, 101.131, 101.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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Components

#1: Protein Autophagy-related protein 13,Gamma-aminobutyric acid receptor-associated protein / GABA(A) receptor-associated protein / MM46


Mass: 16182.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG13, KIAA0652, GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli) / References: UniProt: O75143, UniProt: O95166
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M NaCl, 10% PEG 8000, 0.1M Na K phosphate 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.14→50.565 Å / Num. obs: 62488 / % possible obs: 99.9 % / Redundancy: 17.9 % / Biso Wilson estimate: 15.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.01 / Rrim(I) all: 0.04 / Net I/σ(I): 23.7
Reflection shellResolution: 1.14→1.18 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.82 / Mean I/σ(I) obs: 1 / Num. unique obs: 6252 / CC1/2: 0.55 / Rpim(I) all: 0.54 / Rrim(I) all: 1.9 / % possible all: 99.9

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Processing

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

1gnu


Resolution: 1.14→50.565 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.99
RfactorNum. reflection% reflection
Rfree0.1853 3078 4.93 %
Rwork0.1672 --
obs0.1681 62466 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.14→50.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 0 171 1253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131267
X-RAY DIFFRACTIONf_angle_d1.2961733
X-RAY DIFFRACTIONf_dihedral_angle_d25.722497
X-RAY DIFFRACTIONf_chiral_restr0.102181
X-RAY DIFFRACTIONf_plane_restr0.011230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1403-1.15810.29431530.30362702X-RAY DIFFRACTION100
1.1581-1.17710.3131470.29352669X-RAY DIFFRACTION100
1.1771-1.19740.27051520.27322685X-RAY DIFFRACTION100
1.1974-1.21910.25461410.25262661X-RAY DIFFRACTION100
1.2191-1.24260.26441470.23152668X-RAY DIFFRACTION100
1.2426-1.2680.23371330.21532671X-RAY DIFFRACTION100
1.268-1.29550.21161380.20122690X-RAY DIFFRACTION100
1.2955-1.32570.2091260.17272678X-RAY DIFFRACTION100
1.3257-1.35880.18381230.15572705X-RAY DIFFRACTION100
1.3588-1.39560.18641450.1532676X-RAY DIFFRACTION100
1.3956-1.43660.15391480.13862663X-RAY DIFFRACTION100
1.4366-1.4830.1541240.12392704X-RAY DIFFRACTION100
1.483-1.5360.16431160.11542727X-RAY DIFFRACTION100
1.536-1.59750.13281500.10812700X-RAY DIFFRACTION100
1.5975-1.67020.1461490.10792651X-RAY DIFFRACTION100
1.6702-1.75830.15471130.11152735X-RAY DIFFRACTION100
1.7583-1.86850.14561430.1192723X-RAY DIFFRACTION100
1.8685-2.01270.14551560.13842678X-RAY DIFFRACTION100
2.0127-2.21530.17521720.15042671X-RAY DIFFRACTION100
2.2153-2.53580.17271420.17112732X-RAY DIFFRACTION100
2.5358-3.19480.22061240.18342757X-RAY DIFFRACTION100
3.1948-50.61530.19611360.18792842X-RAY DIFFRACTION100

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