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- PDB-8adm: Ternary complex of 14-3-3 sigma, Usp8pS718 phosphopeptide and sma... -

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Basic information

Entry
Database: PDB / ID: 8adm
TitleTernary complex of 14-3-3 sigma, Usp8pS718 phosphopeptide and small molecule stabilizer
Components
  • 14-3-3 protein sigma
  • Ubiquitin carboxyl-terminal hydrolase 8
KeywordsSIGNALING PROTEIN / 14-3-3 sigma / Usp8 / small molecule stabilizer
Function / homology
Function and homology information


negative regulation of lysosomal protein catabolic process / acrosomal membrane / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / protein K48-linked deubiquitination / endosome organization / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / positive regulation of amyloid fibril formation / regulation of epidermal cell division ...negative regulation of lysosomal protein catabolic process / acrosomal membrane / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / protein K48-linked deubiquitination / endosome organization / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / positive regulation of amyloid fibril formation / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / mitotic cytokinesis / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / protein deubiquitination / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / negative regulation of keratinocyte proliferation / cellular response to dexamethasone stimulus / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / Regulation of FZD by ubiquitination / positive regulation of cell adhesion / Downregulation of ERBB2:ERBB3 signaling / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Negative regulation of MET activity / cellular response to nerve growth factor stimulus / regulation of protein stability / SH3 domain binding / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / positive regulation of canonical Wnt signaling pathway / regulation of protein localization / positive regulation of cell growth / midbody / Ras protein signal transduction / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / early endosome / regulation of cell cycle / endosome membrane / Ub-specific processing proteases / postsynaptic density / cadherin binding / cysteine-type endopeptidase activity / protein kinase binding / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / proteolysis / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / USP8 WW domain / USP8 dimerisation domain / USP8 dimerisation domain / : / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Ubiquitin specific protease (USP) domain signature 2. ...: / USP8 WW domain / USP8 dimerisation domain / USP8 dimerisation domain / : / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / 14-3-3 domain / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Papain-like cysteine peptidase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-O6C / 14-3-3 protein sigma / Ubiquitin carboxyl-terminal hydrolase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCentorrino, F. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionEuropean Union
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: A Systematic Approach to the Discovery of Protein-Protein Interaction Stabilizers.
Authors: Kenanova, D.N. / Visser, E.J. / Virta, J.M. / Sijbesma, E. / Centorrino, F. / Vickery, H.R. / Zhong, M. / Neitz, R.J. / Brunsveld, L. / Ottmann, C. / Arkin, M.R.
History
DepositionJul 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: 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 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Ubiquitin carboxyl-terminal hydrolase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0363
Polymers27,5482
Non-polymers4881
Water4,306239
1
A: 14-3-3 protein sigma
P: Ubiquitin carboxyl-terminal hydrolase 8
hetero molecules

A: 14-3-3 protein sigma
P: Ubiquitin carboxyl-terminal hydrolase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0726
Polymers55,0964
Non-polymers9762
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area4700 Å2
ΔGint-26 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.095, 96.034, 79.677
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26542.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Ubiquitin carboxyl-terminal hydrolase 8 / Deubiquitinating enzyme 8 / Ubiquitin isopeptidase Y / hUBPy / Ubiquitin thioesterase 8 / Ubiquitin- ...Deubiquitinating enzyme 8 / Ubiquitin isopeptidase Y / hUBPy / Ubiquitin thioesterase 8 / Ubiquitin-specific-processing protease 8


Mass: 1004.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P40818, ubiquitinyl hydrolase 1
#3: Chemical ChemComp-O6C / 1-[2-(4-chloranylphenoxy)-2-methyl-propanoyl]-~{N}-[2-[2-(dimethylamino)ethyldisulfanyl]ethyl]piperidine-4-carboxamide


Mass: 488.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H34ClN3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1M buffer ...Details: 0.1M carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1M buffer system 1 (Imidazole; MES monohydrate) pH 6.5 and 50% precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→39.84 Å / Num. obs: 34318 / % possible obs: 99.4 % / Redundancy: 13.2 % / Biso Wilson estimate: 26.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12.1
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 1.032 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1669 / CC1/2: 0.832

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YWT

1ywt


Resolution: 1.7→39.84 Å / SU ML: 0.1795 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9639 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.222 1762 5.14 %
Rwork0.1847 32528 -
obs0.1866 34290 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.25 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 25 239 2114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911945
X-RAY DIFFRACTIONf_angle_d1.10482629
X-RAY DIFFRACTIONf_chiral_restr0.0484289
X-RAY DIFFRACTIONf_plane_restr0.0062342
X-RAY DIFFRACTIONf_dihedral_angle_d19.31881197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.29341140.2452461X-RAY DIFFRACTION98.28
1.75-1.80.25761430.23682443X-RAY DIFFRACTION98.74
1.8-1.860.26521490.22682439X-RAY DIFFRACTION98.52
1.86-1.920.27191160.22362466X-RAY DIFFRACTION98.74
1.92-20.27761330.21252462X-RAY DIFFRACTION99.05
2-2.090.23731360.20062505X-RAY DIFFRACTION99.21
2.09-2.20.22051320.18392472X-RAY DIFFRACTION99.35
2.2-2.340.19331460.17282487X-RAY DIFFRACTION99.55
2.34-2.520.23341210.1762545X-RAY DIFFRACTION99.7
2.52-2.770.21721620.18632472X-RAY DIFFRACTION99.66
2.77-3.170.22671420.18692538X-RAY DIFFRACTION99.89
3.17-40.21081360.17022558X-RAY DIFFRACTION99.96
4-39.840.20491320.17712680X-RAY DIFFRACTION99.96

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