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- PDB-5d94: Crystal structure of LC3-LIR peptide complex -

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Basic information

Entry
Database: PDB / ID: 5d94
TitleCrystal structure of LC3-LIR peptide complex
Components
  • Microtubule-associated proteins 1A/1B light chain 3B
  • Peptide from FYVE and coiled-coil domain-containing protein 1
KeywordsPROTEIN BINDING/PEPTIDE / FYCO1 / autophagy / LC3 / LIR / PROTEIN BINDING-PEPTIDE complex
Function / homology
Function and homology information


plus-end-directed vesicle transport along microtubule / SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / cellular response to nitrogen starvation / TBC/RABGAPs / positive regulation of autophagosome maturation / organelle membrane / Receptor Mediated Mitophagy ...plus-end-directed vesicle transport along microtubule / SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / cellular response to nitrogen starvation / TBC/RABGAPs / positive regulation of autophagosome maturation / organelle membrane / Receptor Mediated Mitophagy / Macroautophagy / axoneme / autophagosome membrane / autophagosome maturation / mitophagy / autophagosome assembly / autophagosome / endomembrane system / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to starvation / mitochondrial membrane / macroautophagy / autophagy / KEAP1-NFE2L2 pathway / late endosome / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / lysosome / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / Golgi apparatus / mitochondrion / membrane / metal ion binding / cytosol
Similarity search - Function
: / : / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / GOLD domain superfamily / GOLD domain / GOLD domain profile. / FYVE zinc finger ...: / : / 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) / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å
AuthorsTakagi, K. / Mizushima, T. / Johansen, T.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: FYCO1 Contains a C-terminally Extended, LC3A/B-preferring LC3-interacting Region (LIR) Motif Required for Efficient Maturation of Autophagosomes during Basal Autophagy
Authors: Olsvik, H.L. / Lamark, T. / Takagi, K. / Larsen, K.B. / Evjen, G. / vervatn, A. / Mizushima, T. / Johansen, T.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3B
B: Peptide from FYVE and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)16,6162
Polymers16,6162
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-6 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.724, 39.162, 42.756
Angle α, β, γ (deg.)90.00, 115.05, 90.00
Int Tables number4
Space group name H-MP1211

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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: 15121.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZQ8
#2: Protein/peptide Peptide from FYVE and coiled-coil domain-containing protein 1


Mass: 1494.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BQS8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 1.89 Å3/Da / Density % sol: 34.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Potassium thiocyanate, 30%(w/v) Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 17994 / % possible obs: 96.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 49.7
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→19.58 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 1.24 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21473 898 5 %RANDOM
Rwork0.17473 ---
obs0.17672 17088 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.648 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.53→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 0 127 1212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191193
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.9731618
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.30123.72959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70315235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4731511
X-RAY DIFFRACTIONr_chiral_restr0.1420.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021905
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.526→1.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 60 -
Rwork0.193 1154 -
obs--92.74 %

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