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- PDB-6mj7: Crystal structure of p62 ZZ domain in complex with free arginine -

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Basic information

Entry
Database: PDB / ID: 6mj7
TitleCrystal structure of p62 ZZ domain in complex with free arginine
ComponentsSequestosome-1
KeywordsSIGNALING PROTEIN / p62 / ZZ domain / Nt-degron / autophagy / receptor
Function / homology
Function and homology information


brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / intracellular membraneless organelle / aggrephagy / negative regulation of toll-like receptor 4 signaling pathway / amphisome / response to mitochondrial depolarisation / regulation of protein complex stability ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / intracellular membraneless organelle / aggrephagy / negative regulation of toll-like receptor 4 signaling pathway / amphisome / response to mitochondrial depolarisation / regulation of protein complex stability / autophagy of mitochondrion / endosome organization / pexophagy / aggresome / membraneless organelle assembly / regulation of mitochondrion organization / phagophore assembly site / ubiquitin-modified protein reader activity / Nuclear events mediated by NFE2L2 / regulation of canonical NF-kappaB signal transduction / cellular response to stress / K63-linked polyubiquitin modification-dependent protein binding / endosomal transport / Lewy body / temperature homeostasis / autolysosome / negative regulation of ferroptosis / molecular sequestering activity / energy homeostasis / mitophagy / immune system process / negative regulation of protein ubiquitination / protein catabolic process / response to ischemia / signaling adaptor activity / inclusion body / positive regulation of autophagy / ionotropic glutamate receptor binding / SH2 domain binding / autophagosome / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Pexophagy / protein kinase C binding / NRIF signals cell death from the nucleus / macroautophagy / positive regulation of long-term synaptic potentiation / positive regulation of protein localization to plasma membrane / PINK1-PRKN Mediated Mitophagy / sarcomere / ubiquitin binding / protein sequestering activity / molecular condensate scaffold activity / protein import into nucleus / P-body / receptor tyrosine kinase binding / PML body / autophagy / Interleukin-1 signaling / intracellular protein localization / Signaling by ALK fusions and activated point mutants / late endosome / KEAP1-NFE2L2 pathway / sperm midpiece / Neddylation / signaling receptor activity / ubiquitin-dependent protein catabolic process / cell differentiation / protein-macromolecule adaptor activity / intracellular signal transduction / positive regulation of apoptotic process / ubiquitin protein ligase binding / apoptotic process / protein kinase binding / protein-containing complex binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / nucleoplasm / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Ubiquitin associated domain ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Ubiquitin associated domain / 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
Similarity search - Domain/homology
ARGININE / 1,4-DIETHYLENE DIOXIDE / Sequestosome-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.412 Å
AuthorsAhn, J. / Zhang, Y. / Kutateladze, T.G.
CitationJournal: Nat Commun / Year: 2018
Title: ZZ-dependent regulation of p62/SQSTM1 in autophagy.
Authors: Zhang, Y. / Mun, S.R. / Linares, J.F. / Ahn, J. / Towers, C.G. / Ji, C.H. / Fitzwalter, B.E. / Holden, M.R. / Mi, W. / Shi, X. / Moscat, J. / Thorburn, A. / Diaz-Meco, M.T. / Kwon, Y.T. / Kutateladze, T.G.
History
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 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: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2365
Polymers5,8421
Non-polymers3944
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.971, 32.269, 34.941
Angle α, β, γ (deg.)90.00, 122.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-394-

HOH

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Components

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


Mass: 5841.748 Da / Num. of mol.: 1 / Fragment: ZZ-TYPE RESIDUES 120-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Production host: Escherichia coli (E. coli) / References: UniProt: Q13501
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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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: 1.87 Å3/Da / Density % sol: 34.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bicine (pH 9.0), 14% PEG 20K, 4% 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.278 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. obs: 107631 / % possible obs: 98.4 % / Redundancy: 13.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.063 / Net I/σ(I): 83.2
Reflection shellResolution: 1.41→1.43 Å / CC1/2: 0.985

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.412→29.579 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 15.39
Details: Some reflections were omitted or filtered out for refinement due to higher redundancy.
RfactorNum. reflection% reflection
Rfree0.1646 815 10.01 %
Rwork0.1356 --
obs0.1386 8141 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.412→29.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms396 0 20 107 523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005453
X-RAY DIFFRACTIONf_angle_d0.811617
X-RAY DIFFRACTIONf_dihedral_angle_d17.254258
X-RAY DIFFRACTIONf_chiral_restr0.07765
X-RAY DIFFRACTIONf_plane_restr0.00884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4124-1.50090.18541280.14691155X-RAY DIFFRACTION95
1.5009-1.61670.1741390.13861247X-RAY DIFFRACTION100
1.6167-1.77940.18581350.13281215X-RAY DIFFRACTION100
1.7794-2.03680.16171360.1381230X-RAY DIFFRACTION100
2.0368-2.5660.16081390.13831239X-RAY DIFFRACTION100
2.566-29.58530.15481380.13051240X-RAY DIFFRACTION97

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