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- PDB-5wrd: Crystal structure of LC3B in complex with FYCO1 LIR -

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Basic information

Entry
Database: PDB / ID: 5wrd
TitleCrystal structure of LC3B in complex with FYCO1 LIR
Components
  • Microtubule-associated proteins 1A/1B light chain 3B
  • Peptide from FYVE and coiled-coil domain-containing protein 1
KeywordsPROTEIN BINDING / Autophagy
Function / homology
Function and homology information


Receptor Mediated Mitophagy / TBC/RABGAPs / Macroautophagy / Pexophagy / PINK1-PRKN Mediated Mitophagy / plus-end-directed vesicle transport along microtubule / ceramide binding / mucus secretion / KEAP1-NFE2L2 pathway / cellular response to nitrogen starvation ...Receptor Mediated Mitophagy / TBC/RABGAPs / Macroautophagy / Pexophagy / PINK1-PRKN Mediated Mitophagy / plus-end-directed vesicle transport along microtubule / ceramide binding / mucus secretion / KEAP1-NFE2L2 pathway / cellular response to nitrogen starvation / phosphatidylethanolamine binding / positive regulation of autophagosome maturation / microtubule associated complex / positive regulation of mucus secretion / autolysosome / axoneme / autophagosome maturation / autophagosome membrane / mitophagy / autophagosome assembly / autophagosome / endomembrane system / cellular response to starvation / tubulin binding / establishment of localization in cell / mitochondrial membrane / macroautophagy / autophagy / late endosome / cytoplasmic vesicle / microtubule binding / microtubule / lysosome / axon / protein domain specific binding / intracellular membrane-bounded organelle / dendrite / neuronal cell body / ubiquitin protein ligase binding / Golgi apparatus / mitochondrion / membrane / metal ion binding / cytosol
Similarity search - Function
FYVE and coiled-coil domain-containing protein 1 / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / GOLD domain superfamily / GOLD domain / GOLD domain profile. / FYVE zinc finger / FYVE zinc finger ...FYVE and coiled-coil domain-containing protein 1 / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / GOLD domain superfamily / GOLD domain / GOLD domain profile. / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger, FYVE/PHD-type / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
FYVE and coiled-coil domain-containing protein 1 / Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsSakurai, S. / Ohto, U. / Shimizu, T.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: The crystal structure of mouse LC3B in complex with the FYCO1 LIR reveals the importance of the flanking region of the LIR motif
Authors: Sakurai, S. / Tomita, T. / Shimizu, T. / Ohto, U.
History
DepositionDec 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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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 3B
B: Microtubule-associated proteins 1A/1B light chain 3B
C: Peptide from FYVE and coiled-coil domain-containing protein 1
D: Peptide from FYVE and coiled-coil domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8276
Polymers33,6424
Non-polymers1842
Water90150
1
A: Microtubule-associated proteins 1A/1B light chain 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7302
Polymers14,6381
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Microtubule-associated proteins 1A/1B light chain 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7302
Polymers14,6381
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptide from FYVE and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)2,1831
Polymers2,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peptide from FYVE and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)2,1831
Polymers2,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Microtubule-associated proteins 1A/1B light chain 3B
C: Peptide from FYVE and coiled-coil domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9133
Polymers16,8212
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-4 kcal/mol
Surface area7800 Å2
MethodPISA
6
B: Microtubule-associated proteins 1A/1B light chain 3B
D: Peptide from FYVE and coiled-coil domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9133
Polymers16,8212
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-7 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.412, 44.613, 63.582
Angle α, β, γ (deg.)90.00, 120.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 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: 14637.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Map1lc3b, Map1alc3, Map1lc3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CQV6
#2: Protein/peptide Peptide from FYVE and coiled-coil domain-containing protein 1 /


Mass: 2183.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8VDC1
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2M ammonium sulfate, 0.1M sodium citrate tribasic dihydrate (pH 5.6), 0.2M potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 21371 / % possible obs: 98.1 % / Redundancy: 3.4 % / Net I/σ(I): 20.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.974 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24418 1087 5.1 %RANDOM
Rwork0.1881 ---
obs0.19088 20284 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å2-0 Å20.33 Å2
2--0.01 Å20 Å2
3---0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 12 50 2316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192300
X-RAY DIFFRACTIONr_bond_other_d0.0010.022228
X-RAY DIFFRACTIONr_angle_refined_deg1.9951.9733094
X-RAY DIFFRACTIONr_angle_other_deg0.94335128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.995268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60524.355124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68515438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6271520
X-RAY DIFFRACTIONr_chiral_restr0.1290.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02526
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_it3.8093.751084
X-RAY DIFFRACTIONr_mcbond_other3.8063.7481083
X-RAY DIFFRACTIONr_mcangle_it5.0165.5851348
X-RAY DIFFRACTIONr_mcangle_other5.0145.5881349
X-RAY DIFFRACTIONr_scbond_it4.6534.311214
X-RAY DIFFRACTIONr_scbond_other4.6364.3111214
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0086.2581747
X-RAY DIFFRACTIONr_long_range_B_refined8.71129.422503
X-RAY DIFFRACTIONr_long_range_B_other8.70929.432504
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 61 -
Rwork0.265 1379 -
obs--89.78 %

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