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- PDB-1ugm: Crystal Structure of LC3 -

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Basic information

Entry
Database: PDB / ID: 1ugm
TitleCrystal Structure of LC3
ComponentsMicrotubule-associated proteins 1A/1B light chain 3
KeywordsSTRUCTURAL PROTEIN / LC3 / autophagy
Function / homology
Function and homology information


Receptor Mediated Mitophagy / TBC/RABGAPs / Pexophagy / PINK1-PRKN Mediated Mitophagy / KEAP1-NFE2L2 pathway / Macroautophagy / mucus secretion / ceramide binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation ...Receptor Mediated Mitophagy / TBC/RABGAPs / Pexophagy / PINK1-PRKN Mediated Mitophagy / KEAP1-NFE2L2 pathway / Macroautophagy / mucus secretion / ceramide binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / microtubule associated complex / positive regulation of mucus secretion / autophagy of mitochondrion / autolysosome / axoneme / autophagosome membrane / autophagosome maturation / autophagosome assembly / mitophagy / endomembrane system / cellular response to starvation / autophagosome / tubulin binding / establishment of localization in cell / macroautophagy / mitochondrial membrane / autophagy / presynapse / cytoplasmic vesicle / microtubule binding / microtubule / protein domain specific binding / axon / neuronal cell body / dendrite / ubiquitin protein ligase binding / mitochondrion / membrane
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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSugawara, K. / Suzuki, N.N. / Fujioka, Y. / Mizushima, N. / Ohsumi, Y. / Inagaki, F.
Citation
Journal: Genes Cells / Year: 2004
Title: The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8
Authors: Sugawara, K. / Suzuki, N.N. / Fujioka, Y. / Mizushima, N. / Ohsumi, Y. / Inagaki, F.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Crystallization and preliminary X-ray analysis of LC3-I
Authors: Sugawara, K. / Suzuki, N.N. / Fujioka, Y. / Mizushima, N. / Ohsumi, Y. / Inagaki, F.
History
DepositionJun 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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: Microtubule-associated proteins 1A/1B light chain 3


Theoretical massNumber of molelcules
Total (without water)14,5761
Polymers14,5761
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.780, 60.780, 35.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3 / LC3-I


Mass: 14575.725 Da / Num. of mol.: 1 / Fragment: residues -4-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pGEX-6p / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q62625
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.32 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 3350, Sodium citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 7786 / Num. obs: 7786 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.195 / % possible all: 74.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EO6

1eo6


Resolution: 2.05→27.18 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1082264.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 800 10.6 %RANDOM
Rwork0.215 ---
all0.218 7521 --
obs0.218 7521 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.9033 Å2 / ksol: 0.512595 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.94 Å20 Å20 Å2
2---2.94 Å20 Å2
3---5.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.05→27.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 0 65 1008
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 110 11.2 %
Rwork0.24 868 -
obs-978 70.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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