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- PDB-3wao: Crystal structure of Atg13 LIR-fused human LC3B_2-119 -

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Basic information

Entry
Database: PDB / ID: 3wao
TitleCrystal structure of Atg13 LIR-fused human LC3B_2-119
ComponentsAutophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3B
KeywordsAPOPTOSIS / UBIQUITIN-LIKE FOLD / AUTOPHAGY
Function / homology
Function and homology information


Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / SARS-CoV-2 modulates autophagy / ceramide binding / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phosphatidylethanolamine binding / protein kinase regulator activity / phagophore assembly site ...Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / SARS-CoV-2 modulates autophagy / ceramide binding / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phosphatidylethanolamine binding / protein kinase regulator activity / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / autophagosome membrane / axoneme / autophagosome assembly / autophagosome maturation / mitophagy / endomembrane system / positive regulation of autophagy / autophagosome / Pexophagy / cellular response to starvation / protein serine/threonine kinase activator activity / PINK1-PRKN Mediated Mitophagy / macroautophagy / autophagy / mitochondrial membrane / KEAP1-NFE2L2 pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / negative regulation of cell population proliferation / ubiquitin protein ligase binding / protein kinase binding / endoplasmic reticulum membrane / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Autophagy-related protein 13 / HORMA domain superfamily / 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
Autophagy-related protein 13 / Microtubule-associated protein 1 light chain 3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSuzuki, H. / Tabata, K. / Morita, E. / Kawasaki, M. / Kato, R. / Dobson, R.C.J. / Yoshimori, T. / Wakatsuki, S.
CitationJournal: Structure / Year: 2014
Title: Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism.
Authors: Suzuki, H. / Tabata, K. / Morita, E. / Kawasaki, M. / Kato, R. / Dobson, R.C. / Yoshimori, T. / Wakatsuki, S.
History
DepositionMay 6, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Apr 16, 2014Group: Experimental preparation
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3B
B: Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3B
C: Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3B
D: Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)62,2234
Polymers62,2234
Non-polymers00
Water00
1
A: Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)15,5561
Polymers15,5561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)15,5561
Polymers15,5561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)15,5561
Polymers15,5561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)15,5561
Polymers15,5561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.569, 64.569, 130.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Autophagy-related protein 13, 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: 15555.693 Da / Num. of mol.: 4 / Fragment: RESIDUES 436-447, RESIDUES 2-119
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF AUTOPHAGY-RELATED GENE 13 LIR (RESIDUES 436-447), LINKER (GLY SER) AND MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B (RESIDUES 2-119)
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75143, UniProt: Q9GZQ8

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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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium citrate tribasic dihydrate 10% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→43.44 Å / Num. obs: 16435 / % possible obs: 99.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.4
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2372 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VTU

3vtu


Resolution: 2.6→43.44 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.883 / SU B: 37.124 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29404 827 5 %RANDOM
Rwork0.22254 ---
obs0.22608 15570 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.477 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å20 Å2
2---2.33 Å20 Å2
3---4.65 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 0 0 4113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194190
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.975641
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6315494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.15623.915212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70515810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6841536
X-RAY DIFFRACTIONr_chiral_restr0.1120.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213131
X-RAY DIFFRACTIONr_gen_planes_other
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 56 -
Rwork0.326 1113 -
obs--98.9 %
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)
11.4562-0.98280.44452.1569-0.97830.60680.1845-0.0625-0.1441-0.0632-0.00180.05970.0451-0.0296-0.18270.1928-0.0192-0.03620.14760.02130.15414.392-38.101-32.72
23.5872-2.4051.15781.6833-0.77320.403-0.1494-0.22410.44650.01610.0594-0.31580.0127-0.10930.090.1886-0.0061-0.00430.1263-0.02540.2898-21.20111.3679-28.5657
32.3804-1.28960.462.8485-0.5050.81020.12070.0795-0.0627-0.2545-0.0135-0.3154-0.1143-0.0859-0.10720.0933-0.00880.04960.117-0.04350.212311.072-2.796-35.086
41.4920.19470.64320.1784-0.26471.2229-0.07360.2055-0.03460.03240.0532-0.05010.0298-0.01520.02040.2601-0.0332-0.00160.1803-0.01510.0966-18.3525-28.0324-31.7534
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 135
2X-RAY DIFFRACTION2B10 - 133
3X-RAY DIFFRACTION3C10 - 133
4X-RAY DIFFRACTION4D11 - 134

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