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- PDB-2k6q: LC3 p62 complex structure -

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Basic information

Entry
Database: PDB / ID: 2k6q
TitleLC3 p62 complex structure
Components
  • Microtubule-associated proteins 1A/1B light chain 3B
  • p62_peptide from Sequestosome-1
KeywordsAPOPTOSIS INHIBITOR/APOPTOSIS / LC3 / p62 / Alternative splicing / Autophagy / Cytoplasm / Cytoplasmic vesicle / Lipoprotein / Membrane / Microtubule / Ubl conjugation pathway / Apoptosis / Differentiation / Endosome / Immune response / Metal-binding / Nucleus / Phosphoprotein / Zinc / Zinc-finger / APOPTOSIS INHIBITOR-APOPTOSIS COMPLEX
Function / homology
Function and homology information


Receptor Mediated Mitophagy / Interleukin-1 signaling / TBC/RABGAPs / Pexophagy / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / p75NTR recruits signalling complexes / KEAP1-NFE2L2 pathway / PINK1-PRKN Mediated Mitophagy / brown fat cell proliferation ...Receptor Mediated Mitophagy / Interleukin-1 signaling / TBC/RABGAPs / Pexophagy / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / p75NTR recruits signalling complexes / KEAP1-NFE2L2 pathway / PINK1-PRKN Mediated Mitophagy / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / Macroautophagy / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / ceramide binding / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / mucus secretion / pexophagy / regulation of protein complex stability / endosome organization / non-membrane-bounded organelle assembly / molecular sequestering activity / cellular response to nitrogen starvation / phosphatidylethanolamine binding / phagophore assembly site / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / positive regulation of mucus secretion / microtubule associated complex / autolysosome / K63-linked polyubiquitin modification-dependent protein binding / intracellular non-membrane-bounded organelle / temperature homeostasis / immune system process / axoneme / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / autophagosome / endomembrane system / positive regulation of autophagy / energy homeostasis / signaling adaptor activity / inclusion body / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / cellular response to starvation / sarcomere / tubulin binding / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / establishment of localization in cell / response to ischemia / mitochondrial membrane / macroautophagy / protein kinase C binding / positive regulation of protein localization to plasma membrane / ionotropic glutamate receptor binding / P-body / protein catabolic process / PML body / autophagy / protein import into nucleus / late endosome / protein-macromolecule adaptor activity / signaling receptor activity / cytoplasmic vesicle / microtubule binding / microtubule / transcription by RNA polymerase II / cell differentiation / positive regulation of protein phosphorylation / protein domain specific binding / axon / neuronal cell body / apoptotic process / ubiquitin protein ligase binding / dendrite / protein-containing complex binding / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / zinc ion binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin associated domain ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin associated domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Sequestosome-1 / Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsNoda, N. / Kumeta, H. / Nakatogawa, H. / Satoo, K. / Adachi, W. / Ishii, J. / Fujioka, Y. / Ohsumi, Y. / Inagaki, F.
CitationJournal: To be Published
Title: Structural basis of target recognition by ATG8/LC3 during selective autophagy
Authors: Noda, N. / Kumeta, H. / Nakatogawa, H. / Adachi, K. / Adachi, W. / Ishii, J. / Fujioka, Y. / Ohsumi, Y. / Inagaki, F.
History
DepositionJul 17, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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: p62_peptide from Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)16,1322
Polymers16,1322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3B / LC3 / Microtubule-associated protein 1 light chain 3 beta / MAP1A/1B light chain 3 B / MAP1A/MAP1B ...LC3 / Microtubule-associated protein 1 light chain 3 beta / MAP1A/1B light chain 3 B / MAP1A/MAP1B LC3 B / MAP1 light chain 3-like protein 2 / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B


Mass: 14251.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species: norvegicus / Gene: Map1lc3b, Map1alc3, Map1lc3 / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: Q62625
#2: Protein/peptide p62_peptide from Sequestosome-1 / Ubiquitin-binding protein p62 / Protein kinase C-zeta-interacting protein / PKC-zeta-interacting protein


Mass: 1880.942 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species: norvegicus / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: O08623

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D (H)CCH-TOCSY
1413D 1H-13C NOESY
1513D 1H-15N NOESY
1613D HNCA
1713D HN(CA)HA
1813D HBHA(CO)NH
1913D C(CO)NH
11013D HNCO
11113D CCH-TOCSY
11212D (HB)CB(CGCD)HD
11312D HbCbHcCdCeHe
11422D 1H-15N HSQC
11522D 1H-13C HSQC
11623D HNCO
11723D HNCA
11823D CBCA(CO)NH
11923D HBHA(CO)NH
12023D (H)CCH-TOCSY
12123D 1H-15N NOESY
12223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-99% 13C; U-99% 15N] LC3, 1.2 mM p62 peptide, 25 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-99% 13C; U-99% 15N] p62 peptide, 1.2 mM LC3, 25 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMLC3[U-99% 13C; U-99% 15N]1
1.2 mMp62 peptide1
25 mMsodium phosphate1
100 mMsodium chloride1
0.8 mMp62 peptide[U-99% 13C; U-99% 15N]2
1.2 mMLC32
25 mMsodium phosphate2
100 mMsodium chloride2
Sample conditionsIonic strength: 0.125 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddardpeak picking
Sparky3.11Goddardrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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