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- PDB-5ypf: p62/SQSTM1 ZZ domain with Trp-peptide -

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Basic information

Entry
Database: PDB / ID: 5ypf
Titlep62/SQSTM1 ZZ domain with Trp-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 / protein localization to perinuclear region of cytoplasm / brown fat cell proliferation / 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 / protein localization to perinuclear region of cytoplasm / brown fat cell proliferation / 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 / intracellular membraneless organelle / endoplasmic reticulum chaperone complex / aggrephagy / response to mitochondrial depolarisation / negative regulation of IRE1-mediated unfolded protein response / negative regulation of toll-like receptor 4 signaling pathway / regulation of IRE1-mediated unfolded protein response / amphisome / PERK regulates gene expression / protein folding in endoplasmic reticulum / regulation of protein complex stability / cerebellar Purkinje cell layer development / misfolded protein binding / endosome organization / autophagy of mitochondrion / pexophagy / post-translational protein targeting to membrane, translocation / membraneless organelle assembly / phagophore assembly site / regulation of mitochondrion organization / ubiquitin-modified protein reader activity / regulation of canonical NF-kappaB signal transduction / Modulation of host responses by IFN-stimulated genes / Nuclear events mediated by NFE2L2 / aggresome / K63-linked polyubiquitin modification-dependent protein binding / endosomal transport / ER overload response / IRE1-mediated unfolded protein response / cellular response to stress / Lewy body / negative regulation of PERK-mediated unfolded protein response / temperature homeostasis / endoplasmic reticulum-Golgi intermediate compartment / non-chaperonin molecular chaperone ATPase / autolysosome / negative regulation of ferroptosis / intracellular membrane-bounded organelle / Regulation of HSF1-mediated heat shock response / molecular sequestering activity / protein serine/threonine kinase inhibitor activity / immune system process / negative regulation of protein-containing complex assembly / cellular response to glucose starvation / mitophagy / energy homeostasis / endoplasmic reticulum unfolded protein response / ERAD pathway / heat shock protein binding / inclusion body / signaling adaptor activity / negative regulation of protein ubiquitination / protein folding chaperone / substantia nigra development / positive regulation of autophagy / cellular response to interleukin-4 / ionotropic glutamate receptor binding / autophagosome / SH2 domain binding / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Pexophagy / response to endoplasmic reticulum stress / NRIF signals cell death from the nucleus / response to ischemia / positive regulation of protein ubiquitination / protein kinase C binding / positive regulation of long-term synaptic potentiation / sarcomere / PINK1-PRKN Mediated Mitophagy / protein catabolic process / positive regulation of protein localization to plasma membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / ubiquitin binding / P-body / ATP-dependent protein folding chaperone / protein sequestering activity / negative regulation of transforming growth factor beta receptor signaling pathway / molecular condensate scaffold activity / PML body / receptor tyrosine kinase binding / autophagy / Interleukin-1 signaling / protein import into nucleus / Signaling by ALK fusions and activated point mutants / melanosome
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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / 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 superfamily / Zinc finger ZZ-type 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: 2.951 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
C: 78 kDa glucose-regulated protein,Sequestosome-1
D: 78 kDa glucose-regulated protein,Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,69312
Polymers26,1694
Non-polymers5238
Water00
1
A: 78 kDa glucose-regulated protein,Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6733
Polymers6,5421
Non-polymers1312
Water0
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)6,6733
Polymers6,5421
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 78 kDa glucose-regulated protein,Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6733
Polymers6,5421
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 78 kDa glucose-regulated protein,Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6733
Polymers6,5421
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.964, 114.964, 114.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
78 kDa glucose-regulated protein,Sequestosome-1 / GRP-78 / Endoplasmic reticulum lumenal Ca(2+)-binding protein grp78 / Heat shock 70 kDa protein 5 / ...GRP-78 / Endoplasmic reticulum lumenal Ca(2+)-binding protein grp78 / Heat shock 70 kDa protein 5 / Immunoglobulin heavy chain-binding protein / BiP / EBI3-associated protein of 60 kDa / p60 / Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / Ubiquitin-binding protein p62


Mass: 6542.330 Da / Num. of mol.: 4
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.: 8 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTrp (-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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 2000, Tris

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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: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.953→40.65 Å / Num. obs: 5464 / % possible obs: 99.9 % / Redundancy: 10.6 % / Net I/σ(I): 50

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.951→40.646 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2854 528 9.66 %
Rwork0.2395 --
obs0.2438 5464 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.951→40.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 8 0 1418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061442
X-RAY DIFFRACTIONf_angle_d1.0871950
X-RAY DIFFRACTIONf_dihedral_angle_d13.197850
X-RAY DIFFRACTIONf_chiral_restr0.065208
X-RAY DIFFRACTIONf_plane_restr0.006256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9507-3.24750.34211280.27911225X-RAY DIFFRACTION100
3.2475-3.71720.37211290.27841217X-RAY DIFFRACTION100
3.7172-4.68220.27291300.23451222X-RAY DIFFRACTION100
4.6822-40.64970.25091410.21741272X-RAY DIFFRACTION99

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