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- PDB-5dpr: Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121 -

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Basic information

Entry
Database: PDB / ID: 5dpr
TitleCrystal structure of PLEKHM1 LIR-fused human LC3A_2-121
ComponentsPleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A
KeywordsPROTEIN BINDING / Autophagy / PLEKHM1 / Atg8 / LC3 / GABARAP / chimeric protein
Function / homology
Function and homology information


cellular response to oxygen-glucose deprivation / late endosome to lysosome transport / autophagosome-lysosome fusion / autolysosome membrane / SMAD protein signal transduction / lysosome localization / autophagy of mitochondrion / phosphatidylethanolamine binding / positive regulation of bone resorption / cellular response to nitrogen starvation ...cellular response to oxygen-glucose deprivation / late endosome to lysosome transport / autophagosome-lysosome fusion / autolysosome membrane / SMAD protein signal transduction / lysosome localization / autophagy of mitochondrion / phosphatidylethanolamine binding / positive regulation of bone resorption / cellular response to nitrogen starvation / positive regulation of ruffle assembly / Receptor Mediated Mitophagy / response to iron(II) ion / Macroautophagy / p38MAPK cascade / organelle membrane / autolysosome / autophagosome membrane / autophagosome assembly / autophagosome maturation / mitophagy / JNK cascade / autophagosome / cellular response to amino acid starvation / cellular response to copper ion / cellular response to starvation / PINK1-PRKN Mediated Mitophagy / macroautophagy / phospholipid binding / response to lead ion / cellular response to hydrogen peroxide / late endosome membrane / late endosome / protein transport / microtubule binding / microtubule / lysosome / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
PLEKHM1, PH domain / : / : / Rubicon Homology Domain / Rubicon Homology Domain / DUF4206 / RUN / RUN domain / RUN domain superfamily / RUN domain ...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
Microtubule-associated protein 1 light chain 3 alpha / Pleckstrin homology domain-containing family M member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

Downloads & links

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Assembly

Deposited unit
A: Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A
B: Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A
C: Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A
D: Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A


Theoretical massNumber of molelcules
Total (without water)63,7284
Polymers63,7284
Non-polymers00
Water75742
1
A: Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A


Theoretical massNumber of molelcules
Total (without water)15,9321
Polymers15,9321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A


Theoretical massNumber of molelcules
Total (without water)15,9321
Polymers15,9321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A


Theoretical massNumber of molelcules
Total (without water)15,9321
Polymers15,9321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A


Theoretical massNumber of molelcules
Total (without water)15,9321
Polymers15,9321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.700, 63.082, 84.924
Angle α, β, γ (deg.)90.00, 100.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A / PH domain-containing family M member 1 / 162 kDa adapter protein / AP162 / Autophagy-related ...PH domain-containing family M member 1 / 162 kDa adapter protein / AP162 / Autophagy-related protein LC3 A / Autophagy-related ubiquitin-like modifier LC3 A / MAP1 light chain 3-like protein 1 / MAP1A/MAP1B light chain 3 A / MAP1A/MAP1B LC3 A / Microtubule-associated protein 1 light chain 3 alpha


Mass: 15932.104 Da / Num. of mol.: 4
Fragment: UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLEKHM1, KIAA0356, MAP1LC3A / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y4G2, UniProt: Q9H492
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M Bis Tris, pH 5.5, 25% w/v Polyethlene glycol 3,350

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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: Apr 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→45.57 Å / Num. obs: 22767 / % possible obs: 100 % / Redundancy: 3.8 % / Net I/σ(I): 7.1
Reflection shellResolution: 2.5→2.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.614 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.567 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 1190 5.23 %
Rwork0.2179 --
obs0.2202 22758 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→45.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 0 42 4128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064176
X-RAY DIFFRACTIONf_angle_d1.0775651
X-RAY DIFFRACTIONf_dihedral_angle_d15.271601
X-RAY DIFFRACTIONf_chiral_restr0.04620
X-RAY DIFFRACTIONf_plane_restr0.005741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60010.31151300.29482397X-RAY DIFFRACTION100
2.6001-2.71850.37561410.27892366X-RAY DIFFRACTION100
2.7185-2.86180.33721220.27812397X-RAY DIFFRACTION100
2.8618-3.0410.30431360.26062353X-RAY DIFFRACTION100
3.041-3.27580.29451510.25732380X-RAY DIFFRACTION100
3.2758-3.60530.3011370.23492360X-RAY DIFFRACTION100
3.6053-4.12670.2291240.19592412X-RAY DIFFRACTION100
4.1267-5.1980.1711200.16162443X-RAY DIFFRACTION100
5.198-45.57490.24821290.20012460X-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)
10.6047-0.61630.36780.9851-0.99711.54530.1049-0.0759-0.04640.2923-0.2026-0.3379-0.28650.1792-0.3210.13060.0207-0.03510.42430.1370.3335-9.5449-14.676738.0538
20.31110.13020.24430.5663-0.18280.33040.1201-0.65020.07420.3053-0.13350.1581-0.00020.25740.00140.2334-0.02110.05640.4101-0.09630.2327-22.24564.367249.1031
30.55470.7403-0.66160.8535-0.5151.2843-0.086-0.22590.3921-0.02510.12020.04810.21770.45710.00560.2416-0.0519-0.00870.2603-0.03370.3553-12.448.084139.4082
41.3149-0.3149-0.11930.20280.41721.0341-0.48080.23341.0067-0.36130.3218-0.0129-0.42750.8461-0.00740.4217-0.1314-0.01520.4340.08120.2628-5.609311.093831.3342
51.8593-1.7764-0.09321.91120.26160.15380.59790.42140.2091-0.4048-0.40980.2387-0.3608-0.23460.15020.60280.08310.04730.2030.18631.0283-17.84615.699129.5154
61.04680.60670.0430.68010.16280.06370.20350.09580.8723-0.23160.04660.75140.112-0.33550.05260.34730.0207-0.01290.26590.03890.4355-20.499710.153335.8496
70.334-0.0375-0.14530.25180.30430.39770.31150.10350.04350.3055-0.12470.1464-0.0683-0.13470.66630.03070.39790.28390.2802-0.40350.293-38.21584.269238.5889
81.09970.65430.1491.9449-0.1972.1367-0.0125-0.2122-0.3150.0276-0.0421-0.22930.0322-0.5262-0.25220.1874-0.03660.02190.20250.05130.2515-34.3696-17.988639.0168
92.9638-0.70790.76921.66870.09250.26120.23910.7957-1.0790.53630.23740.706-0.26420.57310.130.5709-0.00340.18830.5056-0.15670.2674-27.7468-25.331229.2883
100.2486-0.1963-0.08821.1676-0.0940.5954-0.32270.236-0.45750.23960.3017-0.3387-0.2716-0.1055-0.02480.19630.01230.06740.31750.02850.3647-27.9904-19.131633.3729
111.25141.022-0.70860.8738-0.62870.45160.0669-0.39360.5319-0.10030.59220.14670.18140.36470.32480.34160.1163-0.08980.3116-0.11780.2485-24.702317.87323.642
122.4448-1.6169-0.45681.11820.46630.815-0.2610.2169-0.6683-1.04660.20850.06450.0079-0.13160.21470.4224-0.05740.18190.2587-0.12810.2246-5.80664.8986-7.0211
131.07430.6964-0.05331.50020.79080.9269-0.0073-0.2022-0.2575-0.05940.0706-0.2399-0.25670.2465-0.00020.3072-0.0483-0.00260.29890.05230.1902-1.122717.65596.1148
140.33050.12510.09740.03360.20261.7733-0.03-0.3765-0.59990.26240.0394-0.88541.18520.3523-0.00250.34670.1066-0.02710.47590.05670.66965.595.82038.764
150.56040.33760.04270.17910.08160.37960.12320.0145-0.12140.3016-0.0529-0.0216-0.03790.00820.00910.3461-0.0109-0.01110.25490.05110.1898-4.91419.52669.7171
160.0625-0.21440.08940.8231-0.30860.1256-0.05040.1507-0.30650.35390.20460.7717-0.1170.1150.00530.42030.06920.04870.3252-0.0190.3689-6.2981-10.83563.2876
170.97880.965-0.57041.7553-0.01190.5006-0.0976-0.02040.2513-0.25280.21030.40380.12240.06720.00740.2787-0.0189-0.12050.24110.07450.3526-27.4551-3.9223-1.3913
180.0846-0.07380.11740.369-0.08310.2430.2503-0.3018-0.26790.3672-0.22680.90070.6551-0.11050.00210.5144-0.14430.09320.4089-0.00790.3499-31.5812-14.880710.4249
190.98150.95690.52250.91140.4370.3112-0.0442-0.49410.67730.32670.04291.2141-0.7116-0.1241-0.19340.25020.09380.09210.4097-0.03650.6158-32.3309-0.55798.042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 93 )
5X-RAY DIFFRACTION5chain 'A' and (resid 94 through 105 )
6X-RAY DIFFRACTION6chain 'A' and (resid 106 through 129 )
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 17 )
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 94 )
9X-RAY DIFFRACTION9chain 'B' and (resid 95 through 105 )
10X-RAY DIFFRACTION10chain 'B' and (resid 106 through 132 )
11X-RAY DIFFRACTION11chain 'C' and (resid 6 through 17 )
12X-RAY DIFFRACTION12chain 'C' and (resid 18 through 37 )
13X-RAY DIFFRACTION13chain 'C' and (resid 38 through 94 )
14X-RAY DIFFRACTION14chain 'C' and (resid 95 through 113 )
15X-RAY DIFFRACTION15chain 'C' and (resid 114 through 132 )
16X-RAY DIFFRACTION16chain 'D' and (resid 6 through 17 )
17X-RAY DIFFRACTION17chain 'D' and (resid 18 through 70 )
18X-RAY DIFFRACTION18chain 'D' and (resid 71 through 93 )
19X-RAY DIFFRACTION19chain 'D' and (resid 94 through 129 )

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