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- PDB-6hyl: Structure of PCM1 LIR motif bound to GABARAP -

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Basic information

Entry
Database: PDB / ID: 6hyl
TitleStructure of PCM1 LIR motif bound to GABARAP
ComponentsPericentriolar material 1 protein,Gamma-aminobutyric acid receptor-associated protein
KeywordsSIGNALING PROTEIN / Autophagy / ATG8 / LIR
Function / homology
Function and homology information


protein-containing complex localization to centriolar satellite / intraciliary transport involved in cilium assembly / interkinetic nuclear migration / microtubule anchoring / ciliary transition zone / microtubule anchoring at centrosome / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / regulation of protein complex stability / neuronal stem cell population maintenance ...protein-containing complex localization to centriolar satellite / intraciliary transport involved in cilium assembly / interkinetic nuclear migration / microtubule anchoring / ciliary transition zone / microtubule anchoring at centrosome / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / regulation of protein complex stability / neuronal stem cell population maintenance / GABA receptor binding / positive regulation of intracellular protein transport / cellular response to nitrogen starvation / phosphatidylethanolamine binding / non-motile cilium assembly / TBC/RABGAPs / centrosome cycle / protein localization to centrosome / microtubule associated complex / Macroautophagy / beta-tubulin binding / pericentriolar material / axoneme / smooth endoplasmic reticulum / autophagosome membrane / social behavior / autophagosome assembly / cilium assembly / centriolar satellite / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome / protein targeting / cytoplasmic microtubule organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / ciliary basal body / macroautophagy / neuron migration / microtubule cytoskeleton organization / negative regulation of neurogenesis / Regulation of PLK1 Activity at G2/M Transition / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / apical part of cell / chemical synaptic transmission / cytoplasmic vesicle / microtubule binding / nuclear membrane / microtubule / lysosome / molecular adaptor activity / Golgi membrane / centrosome / synapse / ubiquitin protein ligase binding / protein-containing complex / nucleoplasm / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Pericentriolar material 1 protein / Pericentriolar material 1 protein, C-terminal / Pericentriolar material 1 C terminus / 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 / Pericentriolar material 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.559 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: 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: Pericentriolar material 1 protein,Gamma-aminobutyric acid receptor-associated protein
B: Pericentriolar material 1 protein,Gamma-aminobutyric acid receptor-associated protein


Theoretical massNumber of molelcules
Total (without water)32,3792
Polymers32,3792
Non-polymers00
Water4,216234
1
A: Pericentriolar material 1 protein,Gamma-aminobutyric acid receptor-associated protein


Theoretical massNumber of molelcules
Total (without water)16,1901
Polymers16,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pericentriolar material 1 protein,Gamma-aminobutyric acid receptor-associated protein


Theoretical massNumber of molelcules
Total (without water)16,1901
Polymers16,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.696, 65.977, 95.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pericentriolar material 1 protein,Gamma-aminobutyric acid receptor-associated protein / / hPCM-1 / GABA(A) receptor-associated protein / MM46


Mass: 16189.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCM1, GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15154, UniProt: O95166
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M CaCl2, 0.1 M HEPES pH 7, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→54.32 Å / Num. obs: 49150 / % possible obs: 99 % / Redundancy: 5.2 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Net I/σ(I): 11.1
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4840 / CC1/2: 0.69 / Rpim(I) all: 0.47 / Rrim(I) all: 1.08 / % possible all: 95.7

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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: 1.559→54.32 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.56
RfactorNum. reflection% reflection
Rfree0.2469 2398 4.91 %
Rwork0.199 --
obs0.2013 48800 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.559→54.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 0 234 2361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022281
X-RAY DIFFRACTIONf_angle_d0.5143104
X-RAY DIFFRACTIONf_dihedral_angle_d18.2621397
X-RAY DIFFRACTIONf_chiral_restr0.046330
X-RAY DIFFRACTIONf_plane_restr0.003405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5587-1.59050.47571460.37622538X-RAY DIFFRACTION94
1.5905-1.62510.411490.33942652X-RAY DIFFRACTION98
1.6251-1.66290.31461470.30272657X-RAY DIFFRACTION98
1.6629-1.70450.38961390.2772689X-RAY DIFFRACTION99
1.7045-1.75060.32951260.24712701X-RAY DIFFRACTION99
1.7506-1.80210.31421350.22252725X-RAY DIFFRACTION99
1.8021-1.86030.28321140.20662730X-RAY DIFFRACTION99
1.8603-1.92680.25431320.1942729X-RAY DIFFRACTION100
1.9268-2.00390.25481360.18192746X-RAY DIFFRACTION100
2.0039-2.09510.23581500.17712704X-RAY DIFFRACTION100
2.0951-2.20560.23991470.17662736X-RAY DIFFRACTION100
2.2056-2.34380.24081490.18622740X-RAY DIFFRACTION100
2.3438-2.52470.24851570.18912746X-RAY DIFFRACTION100
2.5247-2.77880.29361380.22774X-RAY DIFFRACTION100
2.7788-3.18090.23151490.20322775X-RAY DIFFRACTION100
3.1809-4.00740.24191360.19082824X-RAY DIFFRACTION100
4.0074-54.35590.19781480.18852936X-RAY DIFFRACTION99

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