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- PDB-5dpt: Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117 -

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Basic information

Entry
Database: PDB / ID: 5dpt
TitleCrystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117
ComponentsPleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,Gamma-aminobutyric acid receptor-associated protein-like 1
KeywordsPROTEIN BINDING / Autophagy / chimeric protein
Function / homology
Function and homology information


glycophagy / late endosome to lysosome transport / autophagosome-lysosome fusion / Tat protein binding / autolysosome membrane / GABA receptor binding / lysosome localization / cellular response to nitrogen starvation / phosphatidylethanolamine binding / positive regulation of ruffle assembly ...glycophagy / late endosome to lysosome transport / autophagosome-lysosome fusion / Tat protein binding / autolysosome membrane / GABA receptor binding / lysosome localization / cellular response to nitrogen starvation / phosphatidylethanolamine binding / positive regulation of ruffle assembly / autolysosome / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome maturation / autophagosome assembly / autophagosome / positive regulation of bone resorption / cytoplasmic vesicle membrane / phospholipid binding / protein transport / late endosome membrane / microtubule / lysosome / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / nucleolus / Golgi apparatus / endoplasmic reticulum / metal ion binding / cytosol
Similarity search - Function
PLEKHM1, PH domain / : / Rubicon Homology Domain / Rubicon Homology Domain / DUF4206 / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. ...PLEKHM1, PH domain / : / Rubicon Homology Domain / Rubicon Homology Domain / DUF4206 / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein-like 1 / Pleckstrin homology domain-containing family M member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsRavichandran, A.C. / Suzuki, H. / Dobson, R.C.J.
CitationJournal: EMBO Rep. / Year: 2017
Title: Structural and functional analysis of the GABARAP interaction motif (GIM).
Authors: Rogov, V.V. / Stolz, A. / Ravichandran, A.C. / Rios-Szwed, D.O. / Suzuki, H. / Kniss, A. / Lohr, F. / Wakatsuki, S. / Dotsch, V. / Dikic, I. / Dobson, R.C. / McEwan, D.G.
History
DepositionSep 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,Gamma-aminobutyric acid receptor-associated protein-like 1
B: Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,Gamma-aminobutyric acid receptor-associated protein-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6504
Polymers31,4132
Non-polymers2362
Water00
1
A: Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,Gamma-aminobutyric acid receptor-associated protein-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8252
Polymers15,7071
Non-polymers1181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,Gamma-aminobutyric acid receptor-associated protein-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8252
Polymers15,7071
Non-polymers1181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.791, 84.791, 105.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,Gamma-aminobutyric acid receptor-associated protein-like 1 / PH domain-containing family M member 1 / 162 kDa adapter protein / AP162 / Early estrogen-regulated ...PH domain-containing family M member 1 / 162 kDa adapter protein / AP162 / Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular epithelial cell protein 1 / GEC-1


Mass: 15706.726 Da / Num. of mol.: 2 / Fragment: UNP Q9Y4G2 627-638, UNP Q9H0R8 2-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLEKHM1, GABARAPL1 / Plasmid: pET30 / Cell line (production host): BL21(de3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y4G2, UniProt: Q9H0R8
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM

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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: 3.48 Å3/Da / Density % sol: 64.69 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 20% w/v Polyethylene glycol 3,350, 0.2 M NaCl, 8% MPD pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→42.826 Å / Num. obs: 10119 / % possible obs: 99.9 % / Redundancy: 10.9 % / Net I/σ(I): 10.6
Reflection shellResolution: 2.9→3.03 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2.9→42.826 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 562 5.56 %
Rwork0.214 --
obs0.2162 10105 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→42.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 16 0 1949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032004
X-RAY DIFFRACTIONf_angle_d0.7782741
X-RAY DIFFRACTIONf_dihedral_angle_d12.428704
X-RAY DIFFRACTIONf_chiral_restr0.03294
X-RAY DIFFRACTIONf_plane_restr0.004361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.19190.36991490.30812317X-RAY DIFFRACTION100
3.1919-3.65360.36661440.26192349X-RAY DIFFRACTION100
3.6536-4.60230.24811390.21072381X-RAY DIFFRACTION100
4.6023-42.83030.21361300.192496X-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)
15.5499-0.41360.13829.41661.19565.95430.34290.8761-0.4493-1.78440.4018-0.62720.63970.956-0.67310.9850.0793-0.06360.9923-0.31690.6708-41.216919.014-9.8339
210.61930.9269-0.00243.94551.32179.81680.10411.5992-1.0728-0.03830.0652-1.277-0.07811.482-0.41660.724-0.0529-0.10250.8853-0.31050.8555-35.350828.1489-3.873
38.37633.55320.13847.642.08399.18310.61730.1703-0.5070.3586-0.1274-0.07470.01710.2089-0.49430.5081-0.0305-0.07520.5434-0.03560.4421-42.615830.06862.0076
49.6469-3.69621.6048.1905-3.19226.3824-0.1803-0.2042-0.27020.506-0.05680.34450.4217-0.20680.24090.4975-0.08140.03840.4636-0.1020.5267-55.03917.7926-10.4149
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:22)
2X-RAY DIFFRACTION2(chain A and resid 23:55)
3X-RAY DIFFRACTION3(chain A and resid 56:121)
4X-RAY DIFFRACTION4(chain B and resid 1:123)

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