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

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Basic information

Entry
Database: PDB / ID: 6hym
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 / microtubule anchoring at centrosome / ciliary transition zone / 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 / microtubule anchoring at centrosome / ciliary transition zone / 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 / smooth endoplasmic reticulum / axoneme / autophagosome membrane / social behavior / autophagosome assembly / centriolar satellite / cilium assembly / extrinsic apoptotic signaling pathway via death domain receptors / protein targeting / autophagosome / 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 / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / 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: 1.86 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: Pericentriolar material 1 protein,Gamma-aminobutyric acid receptor-associated protein
B: Pericentriolar material 1 protein,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8107
Polymers32,3792
Non-polymers4305
Water3,459192
1
A: Pericentriolar material 1 protein,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4664
Polymers16,1901
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pericentriolar material 1 protein,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3443
Polymers16,1901
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.873, 80.873, 55.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% w/v PEG 1500, 0.1 M SPG pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.86→45.59 Å / Num. obs: 30131 / % possible obs: 99.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 41.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.01 / Rrim(I) all: 0.02 / Net I/σ(I): 19.7
Reflection shellResolution: 1.86→1.92 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3045 / CC1/2: 0.65 / Rpim(I) all: 0.42 / Rrim(I) all: 0.89 / % possible all: 97.7

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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: 1.86→45.587 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.22
RfactorNum. reflection% reflection
Rfree0.2175 1524 5.08 %
Rwork0.1855 --
obs0.1871 30026 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.86→45.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 28 192 2359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192229
X-RAY DIFFRACTIONf_angle_d1.2323012
X-RAY DIFFRACTIONf_dihedral_angle_d10.6891855
X-RAY DIFFRACTIONf_chiral_restr0.089318
X-RAY DIFFRACTIONf_plane_restr0.008390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8595-1.91960.40181780.3832505X-RAY DIFFRACTION98
1.9196-1.98820.34771290.31692575X-RAY DIFFRACTION99
1.9882-2.06780.27771590.26752525X-RAY DIFFRACTION100
2.0678-2.16190.26741100.23562619X-RAY DIFFRACTION100
2.1619-2.27590.2971650.22472556X-RAY DIFFRACTION100
2.2759-2.41840.28691130.21762592X-RAY DIFFRACTION100
2.4184-2.60510.2761050.20532638X-RAY DIFFRACTION100
2.6051-2.86730.23721390.2092592X-RAY DIFFRACTION100
2.8673-3.28210.20931490.19372597X-RAY DIFFRACTION100
3.2821-4.13460.1791480.16262602X-RAY DIFFRACTION100
4.1346-45.60020.18791290.15062701X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.34390.74860.05690.6210.12991.1733-0.2768-0.26450.0702-0.3675-0.0266-0.1983-0.25850.2132-0.06920.419-0.0343-0.08580.43040.10320.512825.369693.7818-1.5338
21.89020.64150.8261.47110.24211.692-0.1107-0.13330.1083-0.1433-0.12250.0279-0.0873-0.1542-0.00010.3528-0.001-0.06750.37180.0480.398613.086595.2171-8.56
30.7181-0.0271-0.30630.09090.17240.4321-0.0383-0.3413-0.02170.0195-0.0758-0.0154-0.0160.008700.434-0.0542-0.09090.46520.07030.408318.247292.8559-1.9156
40.58180.6874-0.79280.7147-0.36392.7895-0.40840.2634-0.5470.4859-0.06050.64871.4681-1.15-0.17350.3634-0.41120.09810.7872-0.07350.583916.967105.67416.5067
51.76410.0665-1.41161.20880.84532.2344-0.1804-0.044-0.04970.21890.02320.21930.4314-0.4749-0.00210.398-0.09340.03790.44450.0380.333223.4741113.1920.3491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -12 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 117 )
4X-RAY DIFFRACTION4chain 'B' and (resid -11 through 35 )
5X-RAY DIFFRACTION5chain 'B' and (resid 36 through 117 )

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