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- PDB-5yp8: p62/SQSTM1 ZZ domain with Arg-peptide -

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Basic information

Entry
Database: PDB / ID: 5yp8
Titlep62/SQSTM1 ZZ domain with Arg-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 protein folding in endoplasmic reticulum / regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / cerebellum structural organization / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / : / maintenance of protein localization in endoplasmic reticulum ...regulation of protein folding in endoplasmic reticulum / regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / cerebellum structural organization / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / : / maintenance of protein localization in endoplasmic reticulum / cerebellar Purkinje cell layer development / protein targeting to vacuole involved in autophagy / negative regulation of IRE1-mediated unfolded protein response / IRE1alpha activates chaperones / regulation of Ras protein signal transduction / Lewy body / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / aggrephagy / response to mitochondrial depolarisation / amphisome / PERK regulates gene expression / protein folding in endoplasmic reticulum / pexophagy / endosome organization / regulation of protein complex stability / autophagy of mitochondrion / misfolded protein binding / post-translational protein targeting to membrane, translocation / phagophore assembly site / aggresome / regulation of mitochondrion organization / regulation of canonical NF-kappaB signal transduction / ERAD pathway / ubiquitin-modified protein reader activity / K63-linked polyubiquitin modification-dependent protein binding / Nuclear events mediated by NFE2L2 / autolysosome / temperature homeostasis / endosomal transport / immune system process / ER overload response / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / mitophagy / Signaling by ALK fusions and activated point mutants / endoplasmic reticulum-Golgi intermediate compartment / autophagosome / Regulation of HSF1-mediated heat shock response / cellular response to glucose starvation / negative regulation of protein-containing complex assembly / signaling adaptor activity / positive regulation of autophagy / energy homeostasis / : / protein folding chaperone / inclusion body / endoplasmic reticulum unfolded protein response / negative regulation of protein ubiquitination / sperm midpiece / ionotropic glutamate receptor binding / heat shock protein binding / p75NTR recruits signalling complexes / substantia nigra development / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to interleukin-4 / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / SH2 domain binding / response to endoplasmic reticulum stress / sarcomere / protein kinase C binding / ubiquitin binding / positive regulation of protein ubiquitination / positive regulation of long-term synaptic potentiation / response to ischemia / P-body / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / positive regulation of protein localization to plasma membrane / macroautophagy / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / protein catabolic process / protein localization / PML body / receptor tyrosine kinase binding / autophagy / cellular response to reactive oxygen species / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / melanosome / unfolded protein binding / protein-macromolecule adaptor activity / ribosome binding / late endosome / Platelet degranulation / signaling receptor activity
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 profile. / PB1 domain / Endoplasmic reticulum targeting sequence. / Ubiquitin associated domain ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Endoplasmic reticulum targeting sequence. / Ubiquitin associated domain / Zinc finger ZZ-type signature. / 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 / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Heat shock protein 70 family / Hsp70 protein / Zinc finger, ZZ type / Heat shock protein 70kD, C-terminal domain superfamily / 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 / SAD / Resolution: 1.448 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

Downloads & links

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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)13,2886
Polymers13,0272
Non-polymers2624
Water1,33374
1
A: 78 kDa glucose-regulated protein,Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6443
Polymers6,5131
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)6,6443
Polymers6,5131
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.981, 43.948, 66.596
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: 6513.314 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 (bacteria) / Strain (production host): BL21 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsArg (-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: 1.63 Å3/Da / Density % sol: 24.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 400, PEG 300, Tris, NaCl

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.448→19.81 Å / Num. obs: 15275 / % possible obs: 97.3 % / Redundancy: 6.6 % / Net I/σ(I): 49.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.448→19.81 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.53
RfactorNum. reflection% reflection
Rfree0.1942 1529 10.01 %
Rwork0.159 --
obs0.1626 15275 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.448→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 0 4 74 831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012810
X-RAY DIFFRACTIONf_angle_d1.0861072
X-RAY DIFFRACTIONf_dihedral_angle_d20.586297
X-RAY DIFFRACTIONf_chiral_restr0.084113
X-RAY DIFFRACTIONf_plane_restr0.008144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4485-1.49520.33711360.25351223X-RAY DIFFRACTION99
1.4952-1.54870.33491400.23091247X-RAY DIFFRACTION98
1.5487-1.61070.23611380.19441249X-RAY DIFFRACTION99
1.6107-1.68390.21211390.1661238X-RAY DIFFRACTION99
1.6839-1.77270.22161390.15391262X-RAY DIFFRACTION99
1.7727-1.88370.2291400.1551266X-RAY DIFFRACTION100
1.8837-2.02910.22851420.15521276X-RAY DIFFRACTION100
2.0291-2.23320.19811440.13811295X-RAY DIFFRACTION100
2.2332-2.5560.20741430.14541286X-RAY DIFFRACTION100
2.556-3.21910.17591460.14451312X-RAY DIFFRACTION100
3.2191-24.19740.161220.17091092X-RAY DIFFRACTION78

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