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- PDB-7r1o: p62-ZZ domain of the human sequestosome in complex with dusquetide -

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Basic information

Entry
Database: PDB / ID: 7r1o
Titlep62-ZZ domain of the human sequestosome in complex with dusquetide
Components
  • Dusquetide
  • Sequestosome-1
KeywordsSIGNALING PROTEIN / dusquetide / p62 / ZZ domain / IDR / innate immune response / signalling protein
Function / homology
Function and homology information


brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / Lewy body / aggrephagy / response to mitochondrial depolarisation / amphisome / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / Lewy body / aggrephagy / response to mitochondrial depolarisation / amphisome / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly / pexophagy / endosome organization / regulation of protein complex stability / autophagy of mitochondrion / molecular sequestering activity / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / 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 / intracellular non-membrane-bounded organelle / mitophagy / Signaling by ALK fusions and activated point mutants / autophagosome / signaling adaptor activity / positive regulation of autophagy / energy homeostasis / inclusion body / negative regulation of protein ubiquitination / sperm midpiece / ionotropic glutamate receptor binding / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / NRIF signals cell death from the nucleus / molecular condensate scaffold activity / NF-kB is activated and signals survival / 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 / positive regulation of protein localization to plasma membrane / macroautophagy / protein catabolic process / protein localization / PML body / receptor tyrosine kinase binding / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / protein-macromolecule adaptor activity / late endosome / signaling receptor activity / Neddylation / ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / cell differentiation / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / 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 / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / zinc ion binding / nucleoplasm / 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. / PB1 domain / Ubiquitin associated domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / PB1 domain / PB1 domain / PB1 domain profile. / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.202 Å
AuthorsHakansson, M. / Hansson, M. / Logan, D.T. / Rozek, A. / Donini, O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2022
Title: Dusquetide modulates innate immune response through binding to p62.
Authors: Zhang, Y. / Towers, C.G. / Singh, U.K. / Liu, J. / Hakansson, M. / Logan, D.T. / Donini, O. / Kutateladze, T.G.
History
DepositionFeb 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 17, 2022Group: Database references / Derived calculations / Category: atom_type / citation
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Sequestosome-1
BBB: Sequestosome-1
CCC: Sequestosome-1
DDD: Sequestosome-1
EEE: Dusquetide
FFF: Dusquetide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,56114
Polymers24,0386
Non-polymers5238
Water1,838102
1
AAA: Sequestosome-1
BBB: Sequestosome-1
FFF: Dusquetide
hetero molecules


  • defined by author
  • 12.3 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)12,2817
Polymers12,0193
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-14 kcal/mol
Surface area6340 Å2
2
CCC: Sequestosome-1
DDD: Sequestosome-1
EEE: Dusquetide
hetero molecules


  • defined by author
  • 12.3 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)12,2817
Polymers12,0193
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-22 kcal/mol
Surface area6460 Å2
Unit cell
Length a, b, c (Å)124.070, 25.150, 77.530
Angle α, β, γ (deg.)90.000, 124.915, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 5731.634 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13501
#2: Protein/peptide Dusquetide


Mass: 555.690 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14.4% PEG 8000, 0.08 M Na-cacodylate pH 6.5, 0.16 M Ca acetate. 200 nl 18 mg/ml p62-ZZ-dusquetide complex + 100 nl seed solution + 300 nl reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0403 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 7, 2010 / Details: focusing mirrors
RadiationMonochromator: bent single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0403 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 10270 / % possible obs: 98.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.9
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1487 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALA3.3.16data scaling
XSCALEdata scaling
SHELXDE2006/3phasing
BUCCANEER1.4.0phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.202→24.628 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.906 / SU B: 12.577 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.228
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.243 491 4.784 %
Rwork0.1782 9773 -
all0.181 --
obs-10264 98.892 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.717 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å21.283 Å2
2---4.494 Å2-0 Å2
3---0.913 Å2
Refinement stepCycle: LAST / Resolution: 2.202→24.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 8 102 1704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131644
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141514
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.6582234
X-RAY DIFFRACTIONr_angle_other_deg1.2941.5893528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6045212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85520.84571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72415249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.6081510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02343
X-RAY DIFFRACTIONr_nbd_refined0.1880.2320
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21334
X-RAY DIFFRACTIONr_nbtor_refined0.1570.2752
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2744
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.285
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1170.213
X-RAY DIFFRACTIONr_nbd_other0.1280.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1990.213
X-RAY DIFFRACTIONr_mcbond_it1.5482.057853
X-RAY DIFFRACTIONr_mcbond_other1.5452.055852
X-RAY DIFFRACTIONr_mcangle_it2.6533.061057
X-RAY DIFFRACTIONr_mcangle_other2.6533.0631058
X-RAY DIFFRACTIONr_scbond_it1.2852.128791
X-RAY DIFFRACTIONr_scbond_other1.2842.131792
X-RAY DIFFRACTIONr_scangle_it2.1423.1681175
X-RAY DIFFRACTIONr_scangle_other2.1413.1711176
X-RAY DIFFRACTIONr_lrange_it5.15724.3121721
X-RAY DIFFRACTIONr_lrange_other5.12524.2151713
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.202-2.2590.253420.2257150.2277720.8840.89798.0570.191
2.259-2.320.254260.1896900.1927160.8510.9221000.157
2.32-2.3870.229360.1966610.1987000.930.91499.57140.16
2.387-2.460.244290.1856610.1876910.8870.92599.85530.162
2.46-2.5390.266260.1816590.1836890.8890.9399.41940.152
2.539-2.6280.275280.1895970.1936280.880.92499.52230.164
2.628-2.7260.271320.1885880.1926220.8740.92999.67850.162
2.726-2.8350.267280.1845920.1886220.9050.92899.67850.16
2.835-2.960.251180.1835410.1865590.9310.9371000.165
2.96-3.1020.186330.1555380.1575740.9490.95399.47730.143
3.102-3.2670.243300.1745070.1785390.9320.9599.62890.16
3.267-3.4610.226270.1654680.1684970.9410.95999.59760.159
3.461-3.6950.208190.1854620.1864830.9430.95199.58590.178
3.695-3.9840.181190.1634190.1644440.940.95598.64870.162
3.984-4.3520.242190.1653930.1694170.9390.95898.8010.165
4.352-4.8470.205130.133630.1323830.950.97298.17230.132
4.847-5.5610.269230.1793040.1853330.9360.95898.19820.188
5.561-6.7260.238210.2022690.2052990.9550.94196.990.213
6.726-9.1760.372150.2062140.2122370.80.94496.62450.216
9.176-24.6280.38270.2171320.2241620.9060.95585.80250.237
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.55410.0583-0.57433.1721-0.09770.6062-0.0467-0.0183-0.0204-0.0160.0367-0.04790.0241-0.01250.010.09160.01330.04750.19380.00030.028328.3006-10.309610.0504
21.16050.02960.40335.5708-0.58270.7608-0.10940.4389-0.14540.89620.0528-0.7203-0.2615-0.13650.05660.18480.0278-0.10760.312-0.07360.111735.9218-0.510421.1671
32.00142.88040.13576.3168-0.2260.1142-0.18770.05480.5512-0.54850.21411.19480.05620.0438-0.02640.06560.019-0.08410.19970.07530.2721-0.819413.022112.4758
40.2477-0.3518-0.41812.3956-0.04910.9745-0.0101-0.0182-0.02440.04010.00120.23130.05560.12430.0090.1403-0.00310.10270.18090.00260.09379.27693.397321.3794
511.67822.929-1.39761.14180.31211.2462-0.2631-0.33480.10690.09120.12930.10910.28740.37260.13380.14050.05550.02330.14790.01290.05718.9198-1.111827.9685
63.70072.24054.086110.716-0.09745.2197-0.2237-0.3936-0.0731-0.48310.52510.7301-0.1369-0.6345-0.30140.1093-0.0266-0.00340.20760.07150.071320.8908-13.81342.3977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA120 - 172
2X-RAY DIFFRACTION2ALLBBB124 - 171
3X-RAY DIFFRACTION3ALLCCC121 - 171
4X-RAY DIFFRACTION4ALLDDD120 - 172
5X-RAY DIFFRACTION5ALLEEE1 - 5
6X-RAY DIFFRACTION6ALLFFF1 - 4

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