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- PDB-3eci: Microtubule-associated protein 1 light chain 3 alpha isoform A (M... -

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Basic information

Entry
Database: PDB / ID: 3eci
TitleMicrotubule-associated protein 1 light chain 3 alpha isoform A (MAP1ALC3)
ComponentsMicrotubule-associated protein 1 light chain 3 alpha
KeywordsAPOPTOSIS / UBIQUITIN-LIKE (UB ROLL) / AUTOPHAGY / CYTOPLASM / CYTOPLASMIC VESICLE / LIPOPROTEIN / MEMBRANE / MICROTUBULE / UBL CONJUGATION PATHWAY / STRUCTURAL GENOMICS CONSORTIUM / Alternative splicing
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
Microtubule-associated proteins 1A/1B light chain 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsWalker, J.R. / Davis, T.L. / Mujib, S. / Butler-Cole, C. / Tempel, W. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Dhe-Paganon, S.
CitationJournal: To be Published
Title: Human Autophagy-Related Protein LC3 A
Authors: Walker, J.R. / Davis, T.L. / Mujib, S. / Butler-Cole, C. / Tempel, W. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionAug 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 protein 1 light chain 3 alpha
B: Microtubule-associated protein 1 light chain 3 alpha


Theoretical massNumber of molelcules
Total (without water)28,7012
Polymers28,7012
Non-polymers00
Water0
1
A: Microtubule-associated protein 1 light chain 3 alpha


Theoretical massNumber of molelcules
Total (without water)14,3511
Polymers14,3511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Microtubule-associated protein 1 light chain 3 alpha


Theoretical massNumber of molelcules
Total (without water)14,3511
Polymers14,3511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.066, 80.066, 37.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

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


Mass: 14350.503 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Isoform A (MAPALC3) / Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3A / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Gold / References: UniProt: Q9H492

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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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 32 % PEG 4000, 0.1 M NA ACETATE, PH 4.50, 0.2 M AMMONIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, CRYOPROTECTION 20% GLYCEROL, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97926 / Wavelength: 0.97926 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2007 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.65→40 Å / Num. all: 7058 / Num. obs: 7058 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.059
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.19 / Num. unique all: 682 / Rsym value: 0.713 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UGM

1ugm


Resolution: 2.65→28.31 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 41.44 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R: 10.469 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30379 397 5.7 %RANDOM
Rwork0.23325 ---
obs0.2371 6602 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.478 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2---1.11 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.65→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 0 0 1649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221685
X-RAY DIFFRACTIONr_bond_other_d0.0010.021088
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9662299
X-RAY DIFFRACTIONr_angle_other_deg0.92932665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7465222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73623.11561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55715247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.968159
X-RAY DIFFRACTIONr_chiral_restr0.0720.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211894
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02339
X-RAY DIFFRACTIONr_mcbond_it1.18121128
X-RAY DIFFRACTIONr_mcbond_other0.2192436
X-RAY DIFFRACTIONr_mcangle_it1.96831796
X-RAY DIFFRACTIONr_scbond_it1.2062557
X-RAY DIFFRACTIONr_scangle_it1.8693503
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.306 497 -
Rfree-0 -
obs--100 %
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)
110.2297-0.01140.34515.5985-0.40034.0550.1552-0.1056-0.38750.1206-0.17980.09590.09820.23840.02450.04950.0211-0.00680.12430.01690.0197-60.397637.907610.63
28.58730.46212.59847.83960.93264.92840.40590.1604-0.28890.2096-0.22541.90230.5986-0.4296-0.18050.4923-0.06660.12360.1591-0.03380.6069-59.01529.90646.0783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1166 - 117
2X-RAY DIFFRACTION2BB5 - 1166 - 117

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