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- PDB-3x0w: Crystal structure of PLEKHM1 LIR-fused human LC3B_2-119 -

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Basic information

Entry
Database: PDB / ID: 3x0w
TitleCrystal structure of PLEKHM1 LIR-fused human LC3B_2-119
ComponentsMicrotubule-associated proteins 1A/1B light chain 3B
KeywordsPROTEIN BINDING / UBIQUITIN-LIKE FOLD / AUTOPHAGY / PLEKHM1
Function / homology
Function and homology information


SARS-CoV-2 modulates autophagy / ceramide binding / autophagy of mitochondrion / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / Macroautophagy / Receptor Mediated Mitophagy / axoneme ...SARS-CoV-2 modulates autophagy / ceramide binding / autophagy of mitochondrion / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / Macroautophagy / Receptor Mediated Mitophagy / axoneme / autophagosome maturation / autophagosome membrane / mitophagy / organelle membrane / autophagosome assembly / autophagosome / endomembrane system / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to starvation / mitochondrial membrane / macroautophagy / autophagy / KEAP1-NFE2L2 pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / mitochondrion / cytosol
Similarity search - Function
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
Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsSuzuki, H. / McEwan, D.G. / Popovic, D. / Gubas, A. / Terawaki, S. / Stadel, D. / Coxon, F. / Stegmann, D.M. / Bhogaraju, S. / Maddi, K. ...Suzuki, H. / McEwan, D.G. / Popovic, D. / Gubas, A. / Terawaki, S. / Stadel, D. / Coxon, F. / Stegmann, D.M. / Bhogaraju, S. / Maddi, K. / Kirchhoff, A. / Gatti, E. / Helfrich, M.H. / Behrends, C. / Pierre, P. / Dikic, I. / Wakatsuki, S.
CitationJournal: Mol.Cell / Year: 2015
Title: PLEKHM1 regulates autophagosome-lysosome fusion through HOPS complex and LC3/GABARAP proteins.
Authors: McEwan, D.G. / Popovic, D. / Gubas, A. / Terawaki, S. / Suzuki, H. / Stadel, D. / Coxon, F.P. / Miranda de Stegmann, D. / Bhogaraju, S. / Maddi, K. / Kirchof, A. / Gatti, E. / Helfrich, M.H. ...Authors: McEwan, D.G. / Popovic, D. / Gubas, A. / Terawaki, S. / Suzuki, H. / Stadel, D. / Coxon, F.P. / Miranda de Stegmann, D. / Bhogaraju, S. / Maddi, K. / Kirchof, A. / Gatti, E. / Helfrich, M.H. / Wakatsuki, S. / Behrends, C. / Pierre, P. / Dikic, I.
History
DepositionOct 22, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3B
B: Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)31,4642
Polymers31,4642
Non-polymers00
Water45025
1
A: Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)15,7321
Polymers15,7321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)15,7321
Polymers15,7321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.009, 69.009, 119.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3B / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light ...Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light chain 3-like protein 2 / MAP1A/MAP1B light chain 3 B / MAP1A/MAP1B LC3 B / Microtubule-associated protein 1 light chain 3 beta


Mass: 15731.887 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9GZQ8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Acetate, pH 5.0, 1.4M Ammonium Sulfate, 0.1M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→48.8 Å / Num. obs: 7759 / % possible obs: 92.9 %
Reflection shellResolution: 2.71→2.86 Å / Mean I/σ(I) obs: 3.1 / Num. unique all: 1178 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VTU

3vtu


Resolution: 2.71→48.8 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / SU B: 37.222 / SU ML: 0.352 / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29384 354 4.6 %RANDOM
Rwork0.22442 ---
obs0.22752 7343 92.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.807 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20 Å2
2--2 Å20 Å2
3----4 Å2
Refinement stepCycle: LAST / Resolution: 2.71→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 0 25 2068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192083
X-RAY DIFFRACTIONr_bond_other_d0.0010.022040
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9632810
X-RAY DIFFRACTIONr_angle_other_deg0.80834695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90323.905105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.70515398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5371518
X-RAY DIFFRACTIONr_chiral_restr0.080.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02481
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.713→2.783 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 28 -
Rwork0.287 557 -
obs--99.83 %
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)
11.188-0.0161-0.27720.06080.06010.22830.0736-0.0090.03990.0186-0.0366-0.00430.05780.0293-0.03710.06740.01380.03350.0571-0.00830.13135.135222.214116.2105
21.23050.1297-0.70110.47140.00090.41280.08280.13480.08310.1133-0.0215-0.0209-0.0252-0.077-0.06130.07740.0489-0.00980.0665-0.00770.1256-6.976446.847213.2553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 145
2X-RAY DIFFRACTION2B23 - 145

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