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- PDB-3wal: Crystal structure of human LC3A_2-121 -

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Basic information

Entry
Database: PDB / ID: 3wal
TitleCrystal structure of human LC3A_2-121
ComponentsMicrotubule-associated proteins 1A/1B light chain 3A
KeywordsPROTEIN BINDING / UBIQUITIN-LIKE FOLD / AUTOPHAGY
Function / homology
Function and homology information


cellular response to oxygen-glucose deprivation / autophagy of mitochondrion / cellular response to nitrogen starvation / SMAD protein signal transduction / response to iron(II) ion / autolysosome / Macroautophagy / Receptor Mediated Mitophagy / p38MAPK cascade / autophagosome maturation ...cellular response to oxygen-glucose deprivation / autophagy of mitochondrion / cellular response to nitrogen starvation / SMAD protein signal transduction / response to iron(II) ion / autolysosome / Macroautophagy / Receptor Mediated Mitophagy / p38MAPK cascade / autophagosome maturation / autophagosome membrane / organelle membrane / autophagosome assembly / autophagosome / JNK cascade / cellular response to copper ion / cellular response to amino acid starvation / PINK1-PRKN Mediated Mitophagy / cellular response to starvation / macroautophagy / response to lead ion / phospholipid binding / cellular response to hydrogen peroxide / late endosome / microtubule binding / microtubule / intracellular membrane-bounded organelle / glutamatergic synapse / ubiquitin protein ligase binding / 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
D-MALATE / Microtubule-associated proteins 1A/1B light chain 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8142
Polymers14,6801
Non-polymers1341
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.980, 92.980, 33.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3A / Autophagy-related protein LC3 A / Autophagy-related ubiquitin-like modifier LC3 A / MAP1 light ...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: 14679.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3A / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H492
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2M Sodium malonate, 20% PEG 3350, pH 5.0, VAPOR DIFFUSION, SITTING 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: Oct 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→46.5 Å / Num. obs: 9793 / % possible obs: 100 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 18.2
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1422 / % possible all: 100

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Processing

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

3vtu


Resolution: 2→32.89 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.881 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23693 470 4.8 %RANDOM
Rwork0.18147 ---
obs0.1842 9313 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.092 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---0.74 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 2→32.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 9 88 1057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019988
X-RAY DIFFRACTIONr_bond_other_d0.0010.02967
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.9741330
X-RAY DIFFRACTIONr_angle_other_deg0.91832226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7525114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45623.72551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32915188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.298159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211095
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02232
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 34 -
Rwork0.191 690 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 12.7371 Å / Origin y: 5.358 Å / Origin z: 8.3726 Å
111213212223313233
T0.0344 Å2-0.0037 Å2-0.0115 Å2-0.0722 Å2-0.0263 Å2--0.0773 Å2
L0.8214 °2-0.0091 °2-0.4789 °2-0.7627 °20.1504 °2--1.0809 °2
S-0.0577 Å °0.0397 Å °-0.1597 Å °-0.0252 Å °-0.0386 Å °-0.0432 Å °-0.0208 Å °0.0002 Å °0.0963 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 123
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1A301 - 388

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