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- PDB-5ypg: p62/SQSTM1 ZZ domain with Leu-peptide -

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Basic information

Entry
Database: PDB / ID: 5ypg
Titlep62/SQSTM1 ZZ domain with Leu-peptide
Components78 kDa glucose-regulated protein,Sequestosome-1
KeywordsSIGNALING PROTEIN / Complex / p62/SQSTM1 / ZZ domain / Autophagy / N-end rule
Function / homology
Function and homology information


regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / maintenance of protein localization in endoplasmic reticulum / protein targeting to vacuole involved in autophagy ...regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / maintenance of protein localization in endoplasmic reticulum / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / Lewy body / negative regulation of IRE1-mediated unfolded protein response / cerebellar Purkinje cell layer development / response to mitochondrial depolarisation / aggrephagy / endoplasmic reticulum chaperone complex / negative regulation of toll-like receptor 4 signaling pathway / amphisome / PERK regulates gene expression / protein folding in endoplasmic reticulum / pexophagy / regulation of protein complex stability / endosome organization / misfolded protein binding / membraneless organelle assembly / molecular sequestering activity / post-translational protein targeting to membrane, translocation / ubiquitin-modified protein reader activity / regulation of mitochondrion organization / phagophore assembly site / regulation of canonical NF-kappaB signal transduction / aggresome / Nuclear events mediated by NFE2L2 / negative regulation of ferroptosis / endosomal transport / autophagy of mitochondrion / intracellular membraneless organelle / temperature homeostasis / K63-linked polyubiquitin modification-dependent protein binding / immune system process / ER overload response / non-chaperonin molecular chaperone ATPase / autolysosome / endoplasmic reticulum-Golgi intermediate compartment / chaperone cofactor-dependent protein refolding / mitophagy / Regulation of HSF1-mediated heat shock response / negative regulation of protein-containing complex assembly / cellular response to interleukin-4 / positive regulation of autophagy / cellular response to glucose starvation / signaling adaptor activity / endoplasmic reticulum unfolded protein response / energy homeostasis / inclusion body / ERAD pathway / sperm midpiece / heat shock protein binding / protein folding chaperone / negative regulation of protein ubiquitination / protein sequestering activity / substantia nigra development / ionotropic glutamate receptor binding / autophagosome / p75NTR recruits signalling complexes / response to endoplasmic reticulum stress / sarcomere / NF-kB is activated and signals survival / SH2 domain binding / Pexophagy / NRIF signals cell death from the nucleus / PINK1-PRKN Mediated Mitophagy / ubiquitin binding / positive regulation of protein ubiquitination / positive regulation of long-term synaptic potentiation / response to ischemia / positive regulation of protein localization to plasma membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / protein kinase C binding / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / P-body / molecular condensate scaffold activity / protein catabolic process / PML body / receptor tyrosine kinase binding / autophagy / Interleukin-1 signaling / protein import into nucleus / unfolded protein binding / KEAP1-NFE2L2 pathway / protein localization / Signaling by ALK fusions and activated point mutants / melanosome / late endosome
Similarity search - Function
Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Endoplasmic reticulum targeting sequence. / Ubiquitin associated domain / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / 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 / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Endoplasmic reticulum chaperone BiP / Sequestosome-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsKwon, D.H. / Kim, L. / Song, H.K.
CitationJournal: Nat Commun / Year: 2018
Title: Insights into degradation mechanism of N-end rule substrates by p62/SQSTM1 autophagy adapter.
Authors: Kwon, D.H. / Park, O.H. / Kim, L. / Jung, Y.O. / Park, Y. / Jeong, H. / Hyun, J. / Kim, Y.K. / Song, H.K.
History
DepositionNov 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 27, 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

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Assembly

Deposited unit
A: 78 kDa glucose-regulated protein,Sequestosome-1
B: 78 kDa glucose-regulated protein,Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2006
Polymers12,9392
Non-polymers2624
Water18010
1
A: 78 kDa glucose-regulated protein,Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6003
Polymers6,4691
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 78 kDa glucose-regulated protein,Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6003
Polymers6,4691
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.534, 44.279, 68.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 78 kDa glucose-regulated protein,Sequestosome-1 / GRP-78 / EBI3-associated protein of 60 kDa / p60 / Phosphotyrosine-independent ligand for the Lck ...GRP-78 / EBI3-associated protein of 60 kDa / p60 / Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / Ubiquitin-binding protein p62


Mass: 6469.278 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA5, GRP78, SQSTM1, ORCA, OSIL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11021, UniProt: Q13501
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLeu (-3 position) is synthetic residue generated by special enzyme

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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: 1.66 Å3/Da / Density % sol: 26.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: MgCl2, Sodium cacodylate

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.199→27 Å / Num. obs: 4633 / % possible obs: 98.3 % / Redundancy: 5.2 % / Net I/σ(I): 25.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.199→27 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.19
RfactorNum. reflection% reflection
Rfree0.293 464 10.02 %
Rwork0.2356 --
obs0.2414 4630 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.199→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 4 10 774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005792
X-RAY DIFFRACTIONf_angle_d0.5921050
X-RAY DIFFRACTIONf_dihedral_angle_d12.881468
X-RAY DIFFRACTIONf_chiral_restr0.042114
X-RAY DIFFRACTIONf_plane_restr0.003140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1986-2.51660.31751510.25231354X-RAY DIFFRACTION99
2.5166-3.16980.31691550.25791391X-RAY DIFFRACTION99
3.1698-27.00670.27691580.22261421X-RAY DIFFRACTION96

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