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- PDB-3wap: Crystal structure of Atg13 LIR-fused human LC3C_8-125 -

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Basic information

Entry
Database: PDB / ID: 3wap
TitleCrystal structure of Atg13 LIR-fused human LC3C_8-125
ComponentsAutophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3C
KeywordsPROTEIN TRANSPORT / UBIQUITIN-LIKE FOLD / AUTOPHAGY
Function / homology
Function and homology information


regulation of protein lipidation / Atg1/ULK1 kinase complex / protein exit from endoplasmic reticulum / aggrephagy / response to mitochondrial depolarisation / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / cellular response to nitrogen starvation / phosphatidylethanolamine binding ...regulation of protein lipidation / Atg1/ULK1 kinase complex / protein exit from endoplasmic reticulum / aggrephagy / response to mitochondrial depolarisation / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / cellular response to nitrogen starvation / phosphatidylethanolamine binding / phagophore assembly site / positive regulation of protein targeting to mitochondrion / Macroautophagy / autophagosome maturation / autophagosome membrane / mitophagy / organelle membrane / autophagosome assembly / autophagosome / endomembrane system / positive regulation of autophagy / cellular response to starvation / protein serine/threonine kinase activator activity / macroautophagy / cytoplasmic ribonucleoprotein granule / cytoplasmic vesicle / microtubule / negative regulation of cell population proliferation / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein kinase binding / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Microtubule-associated protein 1A/1B light chain 3C / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / 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 ...Microtubule-associated protein 1A/1B light chain 3C / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / 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 proteins 1A/1B light chain 3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,4021
Polymers15,4021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3C

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


Theoretical massNumber of molelcules
Total (without water)30,8032
Polymers30,8032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1280 Å2
ΔGint-7 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.730, 61.730, 95.881
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3C / Autophagy-related protein LC3 C / Autophagy-related ubiquitin-like modifier LC3 C / MAP1 light ...Autophagy-related protein LC3 C / Autophagy-related ubiquitin-like modifier LC3 C / MAP1 light chain 3-like protein 3 / MAP1A/MAP1B light chain 3 C / MAP1A/MAP1B LC3 C / Microtubule-associated protein 1 light chain 3 gamma


Mass: 15401.719 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 436-447, 8-125
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 3C (RESIDUES 8-125)
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3C / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75143, UniProt: Q9BXW4

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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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Sodium acetate trihydrate, 8% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: 3.1→53.46 Å / Num. obs: 4045 / % possible obs: 98.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.8
Reflection shellResolution: 3.1→3.27 Å / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 2.8 / Num. unique all: 588 / % possible all: 100

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Processing

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

3vtu


Resolution: 3.1→53.46 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 54.548 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27321 185 4.6 %RANDOM
Rwork0.2074 ---
obs0.21045 3854 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 144.718 Å2
Baniso -1Baniso -2Baniso -3
1-6.01 Å23 Å20 Å2
2--6.01 Å20 Å2
3----9.01 Å2
Refinement stepCycle: LAST / Resolution: 3.1→53.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 0 0 1014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021036
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4451.9821398
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8125123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22922.39146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.97915192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9861510
X-RAY DIFFRACTIONr_chiral_restr0.1190.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021769
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: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.53 8 -
Rwork0.35 237 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -16.4349 Å / Origin y: -19.2057 Å / Origin z: -13.3695 Å
111213212223313233
T0.6586 Å20.0373 Å20.0033 Å2-0.3383 Å20.0668 Å2--0.3681 Å2
L3.5329 °2-0.6469 °21.5909 °2-0.6603 °20.6083 °2--2.3893 °2
S-0.1759 Å °-0.0134 Å °0.1124 Å °-0.2899 Å °-0.133 Å °-0.002 Å °-0.5503 Å °-0.0958 Å °0.3088 Å °

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