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- PDB-5yph: p62/SQSTM1 ZZ domain with Ile-peptide -

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Basic information

Entry
Database: PDB / ID: 5yph
Titlep62/SQSTM1 ZZ domain with Ile-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 / brown fat cell proliferation / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / maintenance of protein localization in endoplasmic reticulum / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction ...regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / brown fat cell proliferation / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / maintenance of protein localization in endoplasmic reticulum / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / IRE1alpha activates chaperones / protein targeting to vacuole involved in autophagy / ATF6 (ATF6-alpha) activates chaperone genes / intracellular membraneless organelle / endoplasmic reticulum chaperone complex / aggrephagy / negative regulation of IRE1-mediated unfolded protein response / negative regulation of toll-like receptor 4 signaling pathway / regulation of IRE1-mediated unfolded protein response / response to mitochondrial depolarisation / PERK regulates gene expression / amphisome / protein folding in endoplasmic reticulum / post-translational protein targeting to membrane, translocation / regulation of protein complex stability / cerebellar Purkinje cell layer development / autophagy of mitochondrion / misfolded protein binding / endosome organization / pexophagy / aggresome / membraneless organelle assembly / regulation of mitochondrion organization / phagophore assembly site / Modulation of host responses by IFN-stimulated genes / ubiquitin-modified protein reader activity / Nuclear events mediated by NFE2L2 / regulation of canonical NF-kappaB signal transduction / cellular response to stress / endosomal transport / K63-linked polyubiquitin modification-dependent protein binding / IRE1-mediated unfolded protein response / energy homeostasis / temperature homeostasis / negative regulation of PERK-mediated unfolded protein response / endoplasmic reticulum-Golgi intermediate compartment / Lewy body / non-chaperonin molecular chaperone ATPase / negative regulation of ferroptosis / autolysosome / intracellular membrane-bounded organelle / Regulation of HSF1-mediated heat shock response / molecular sequestering activity / protein serine/threonine kinase inhibitor activity / Dengue Virus Attachment and Entry / response to ischemia / mitophagy / negative regulation of protein-containing complex assembly / cellular response to glucose starvation / immune system process / endoplasmic reticulum unfolded protein response / protein catabolic process / heat shock protein binding / ERAD pathway / negative regulation of protein ubiquitination / protein folding chaperone / substantia nigra development / signaling adaptor activity / inclusion body / ionotropic glutamate receptor binding / positive regulation of autophagy / SH2 domain binding / sperm midpiece / response to endoplasmic reticulum stress / autophagosome / positive regulation of protein ubiquitination / protein import into nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / protein kinase C binding / Pexophagy / NRIF signals cell death from the nucleus / macroautophagy / positive regulation of long-term synaptic potentiation / positive regulation of protein localization to plasma membrane / sarcomere / PINK1-PRKN Mediated Mitophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ubiquitin binding / Maturation of DENV proteins / molecular condensate scaffold activity / protein sequestering activity / P-body / protein refolding / receptor tyrosine kinase binding / PML body / intracellular protein localization / autophagy / Interleukin-1 signaling / :
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. / 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: 1.629 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 1.2Nov 22, 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
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)13,2006
Polymers12,9392
Non-polymers2624
Water2,108117
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)33.658, 33.381, 35.019
Angle α, β, γ (deg.)90.00, 103.61, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 117 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIle (-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 % sol: 16.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: sodium phosphate, potassium phosphate, MgCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.629→17.91 Å / Num. obs: 9011 / % possible obs: 94 % / Redundancy: 3.3 % / Net I/σ(I): 34.7

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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
Starting model: 5YP7

5yp7


Resolution: 1.629→17.909 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18
RfactorNum. reflection% reflection
Rfree0.187 912 10.12 %
Rwork0.1469 --
obs0.1511 9011 93.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.629→17.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms747 0 4 117 868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011762
X-RAY DIFFRACTIONf_angle_d1.3051030
X-RAY DIFFRACTIONf_dihedral_angle_d6.252458
X-RAY DIFFRACTIONf_chiral_restr0.073112
X-RAY DIFFRACTIONf_plane_restr0.011137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.629-1.71480.19061220.11861067X-RAY DIFFRACTION89
1.7148-1.82210.18131210.13031126X-RAY DIFFRACTION92
1.8221-1.96270.18151240.13191138X-RAY DIFFRACTION93
1.9627-2.15990.21911330.1371155X-RAY DIFFRACTION94
2.1599-2.47170.20251350.1491172X-RAY DIFFRACTION96
2.4717-3.11140.19021380.1541190X-RAY DIFFRACTION97
3.1114-17.90960.16741390.15951251X-RAY DIFFRACTION98

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