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- PDB-6i9c: Structure of the OTU domain of OTULIN G281R mutant -

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Basic information

Entry
Database: PDB / ID: 6i9c
TitleStructure of the OTU domain of OTULIN G281R mutant
ComponentsUbiquitin thioesterase otulin
KeywordsHYDROLASE / Met1-specific deubiquitinase
Function / homology
Function and homology information


protein linear deubiquitination / LUBAC complex / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of tumor necrosis factor-mediated signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / cysteine-type peptidase activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of TNFR1 signaling ...protein linear deubiquitination / LUBAC complex / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of tumor necrosis factor-mediated signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / cysteine-type peptidase activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of TNFR1 signaling / Wnt signaling pathway / negative regulation of inflammatory response / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein ubiquitination / innate immune response / proteolysis / cytosol / cytoplasm
Similarity search - Function
Ubiquitin thioesterase otulin / FAM105 / Peptidase family C101
Similarity search - Domain/homology
Ubiquitin thioesterase otulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.77 Å
AuthorsDamgaard, R.B. / Elliott, P.R. / Swatek, K.N. / Maher, E.R. / Stepensky, P. / Elpeleg, O. / Komander, D. / Berkun, Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
European Research Council724804 United Kingdom
CitationJournal: Embo Mol Med / Year: 2019
Title: OTULIN deficiency in ORAS causes cell type-specific LUBAC degradation, dysregulated TNF signalling and cell death.
Authors: Damgaard, R.B. / Elliott, P.R. / Swatek, K.N. / Maher, E.R. / Stepensky, P. / Elpeleg, O. / Komander, D. / Berkun, Y.
History
DepositionNov 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2May 15, 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: Ubiquitin thioesterase otulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6696
Polymers31,2651
Non-polymers4045
Water4,558253
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-5 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.260, 72.437, 93.732
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin thioesterase otulin / Deubiquitinating enzyme otulin / OTU domain-containing deubiquitinase with linear linkage ...Deubiquitinating enzyme otulin / OTU domain-containing deubiquitinase with linear linkage specificity / Ubiquitin thioesterase Gumby


Mass: 31264.961 Da / Num. of mol.: 1 / Mutation: G281R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OTULIN, FAM105B / Production host: Escherichia coli (E. coli) / References: UniProt: Q96BN8, ubiquitinyl hydrolase 1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 100 mM HEPES pH 7.4, 18 % (w/v) PEG 6,000, 1M LiCl

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.77→72.44 Å / Num. obs: 29060 / % possible obs: 98.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.025 / Rrim(I) all: 0.063 / Net I/σ(I): 16.3 / Num. measured all: 189022 / Scaling rejects: 5
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.84 / Num. unique obs: 1655 / CC1/2: 0.739 / Rpim(I) all: 0.354 / Rrim(I) all: 0.913 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.77→57.316 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.97
RfactorNum. reflection% reflection
Rfree0.1786 1480 5.1 %
Rwork0.1623 --
obs0.1632 29002 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.75 Å2 / Biso mean: 33.1145 Å2 / Biso min: 15.88 Å2
Refinement stepCycle: final / Resolution: 1.77→57.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 25 253 2367
Biso mean--54.65 43.57 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062249
X-RAY DIFFRACTIONf_angle_d0.7743065
X-RAY DIFFRACTIONf_chiral_restr0.045337
X-RAY DIFFRACTIONf_plane_restr0.005392
X-RAY DIFFRACTIONf_dihedral_angle_d13.5241398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.77-1.82710.24561400.226924832623100
1.8271-1.89250.24941150.209625162631100
1.8925-1.96820.2671370.200525092646100
1.9682-2.05780.22421540.179224962650100
2.0578-2.16630.19471440.16324902634100
2.1663-2.3020.19811260.159525162642100
2.302-2.47980.1991350.146625302665100
2.4798-2.72930.1841240.15462328245292
2.7293-3.12420.17061340.157825832717100
3.1242-3.93610.16191370.14472377251493
3.9361-57.34610.15061340.16642694282899

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