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- PDB-2zjd: Crystal Structure of LC3-p62 complex -

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Basic information

Entry
Database: PDB / ID: 2zjd
TitleCrystal Structure of LC3-p62 complex
Components
  • Microtubule-associated proteins 1A/1B light chain 3B precursor
  • undecameric peptide from Sequestosome-1
KeywordsApoptosis inhibitor/Apoptosis / p62 / autophagy / LC3 / microtubule-associated protein 1 light chain 3 / Cytoplasm / Cytoplasmic vesicle / Lipoprotein / Membrane / Ubl conjugation pathway / Alternative splicing / Apoptosis / Differentiation / Endosome / Immune response / Metal-binding / Nucleus / Phosphoprotein / Zinc / Zinc-finger / Apoptosis inhibitor-Apoptosis COMPLEX
Function / homology
Function and homology information


Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / SARS-CoV-2 modulates autophagy / protein targeting to vacuole involved in autophagy / Lewy body / negative regulation of toll-like receptor 4 signaling pathway ...Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / SARS-CoV-2 modulates autophagy / protein targeting to vacuole involved in autophagy / Lewy body / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly / NF-kB is activated and signals survival / aggrephagy / response to mitochondrial depolarisation / ceramide binding / amphisome / Interleukin-1 signaling / KEAP1-NFE2L2 pathway / pexophagy / endosome organization / regulation of protein complex stability / autophagy of mitochondrion / cellular response to nitrogen starvation / phosphatidylethanolamine binding / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / K63-linked polyubiquitin modification-dependent protein binding / autolysosome / temperature homeostasis / intracellular non-membrane-bounded organelle / Macroautophagy / Receptor Mediated Mitophagy / immune system process / axoneme / autophagosome maturation / autophagosome membrane / mitophagy / organelle membrane / autophagosome assembly / autophagosome / endomembrane system / signaling adaptor activity / positive regulation of autophagy / energy homeostasis / inclusion body / negative regulation of protein ubiquitination / sperm midpiece / ionotropic glutamate receptor binding / PINK1-PRKN Mediated Mitophagy / molecular condensate scaffold activity / Pexophagy / cellular response to starvation / SH2 domain binding / sarcomere / protein sequestering activity / protein kinase C binding / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / P-body / mitochondrial membrane / transcription coregulator activity / positive regulation of protein localization to plasma membrane / macroautophagy / protein catabolic process / PML body / autophagy / cellular response to reactive oxygen species / protein import into nucleus / KEAP1-NFE2L2 pathway / protein-macromolecule adaptor activity / late endosome / signaling receptor activity / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / transcription by RNA polymerase II / cell differentiation / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / mitochondrion / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / PB1 domain / PB1 domain / PB1 domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / PB1 domain / Ubiquitin associated domain ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / PB1 domain / PB1 domain / PB1 domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / PB1 domain / Ubiquitin associated domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsIchimura, Y. / Kumanomidou, T. / Sou, Y. / Mizushima, T. / Ezaki, J. / Ueno, T. / Kominami, E. / Yamane, T. / Tanaka, K. / Komatsu, M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Basis for Sorting Mechanism of p62 in Selective Autophagy
Authors: Ichimura, Y. / Kumanomidou, T. / Sou, Y.-S. / Mizushima, T. / Ezaki, J. / Ueno, T. / Kominami, E. / Yamane, T. / Tanaka, K. / Komatsu, M.
History
DepositionMar 5, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3B precursor
B: undecameric peptide from Sequestosome-1
C: Microtubule-associated proteins 1A/1B light chain 3B precursor
D: undecameric peptide from Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)32,6234
Polymers32,6234
Non-polymers00
Water5,098283
1
A: Microtubule-associated proteins 1A/1B light chain 3B precursor


Theoretical massNumber of molelcules
Total (without water)15,1211
Polymers15,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: undecameric peptide from Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)1,1901
Polymers1,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Microtubule-associated proteins 1A/1B light chain 3B precursor


Theoretical massNumber of molelcules
Total (without water)15,1211
Polymers15,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: undecameric peptide from Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)1,1901
Polymers1,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Microtubule-associated proteins 1A/1B light chain 3B precursor
B: undecameric peptide from Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)16,3122
Polymers16,3122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-3 kcal/mol
Surface area7650 Å2
MethodPISA
6
C: Microtubule-associated proteins 1A/1B light chain 3B precursor
D: undecameric peptide from Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)16,3122
Polymers16,3122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-5.2 kcal/mol
Surface area7760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.559, 39.592, 78.011
Angle α, β, γ (deg.)90.00, 93.30, 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 precursor / Microtubule-associated protein 1 light chain 3 beta / MAP1A/MAP1B LC3 B / MAP1A/1B light chain 3 B ...Microtubule-associated protein 1 light chain 3 beta / MAP1A/MAP1B LC3 B / MAP1A/1B light chain 3 B / MAP1 light chain 3-like protein 2 / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B


Mass: 15121.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9GZQ8
#2: Protein/peptide undecameric peptide from Sequestosome-1 / Ubiquitin-binding protein p62 / STONE14


Mass: 1190.156 Da / Num. of mol.: 2
Fragment: LC3 recognition sequence (LRS), UNP residue 334-344
Source method: obtained synthetically / Details: This sequence occurs naturally in mouse. / References: UniProt: Q64337
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 23% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Nov 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.55→77.85 Å / Num. obs: 39943 / % possible obs: 98.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 23.9
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.31 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UGM

1ugm


Resolution: 1.56→45.48 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.531 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23766 2005 5 %RANDOM
Rwork0.201 ---
obs0.20281 37918 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.107 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20.71 Å2
2---0.85 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.56→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 0 283 2435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222179
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9592930
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2185254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24123.571112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57415415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4291520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021630
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21035
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21530
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2218
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0371.51325
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67422101
X-RAY DIFFRACTIONr_scbond_it2.2833951
X-RAY DIFFRACTIONr_scangle_it3.5574.5829
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.556→1.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 154 -
Rwork0.23 2597 -
obs--92.81 %

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