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- PDB-5oe7: Structure of OTULIN bound to the Met1-linked diubiquitin activity... -

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Basic information

Entry
Database: PDB / ID: 5oe7
TitleStructure of OTULIN bound to the Met1-linked diubiquitin activity probe
Components
  • Polyubiquitin-C
  • Ubiquitin thioesterase otulin
KeywordsHYDROLASE / deubiquitinase complex OTU
Function / homology
Function and homology information


Downregulation of SMAD2/3:SMAD4 transcriptional activity / Ub-specific processing proteases / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Regulation of activated PAK-2p34 by proteasome mediated degradation / NOTCH1 Intracellular Domain Regulates Transcription / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) ...Downregulation of SMAD2/3:SMAD4 transcriptional activity / Ub-specific processing proteases / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Regulation of activated PAK-2p34 by proteasome mediated degradation / NOTCH1 Intracellular Domain Regulates Transcription / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / TCF dependent signaling in response to WNT / Separation of Sister Chromatids / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Regulation of PLK1 Activity at G2/M Transition / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Stimuli-sensing channels / Constitutive Signaling by NOTCH1 HD Domain Mutants / Downstream TCR signaling / Degradation of beta-catenin by the destruction complex / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Autodegradation of Cdh1 by Cdh1:APC/C / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / Budding and maturation of HIV virion / NOD1/2 Signaling Pathway / TICAM1, RIP1-mediated IKK complex recruitment / DDX58/IFIH1-mediated induction of interferon-alpha/beta / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / SCF(Skp2)-mediated degradation of p27/p21 / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Membrane binding and targetting of GAG proteins / Assembly Of The HIV Virion / APC-Cdc20 mediated degradation of Nek2A / Vpu mediated degradation of CD4 / Vif-mediated degradation of APOBEC3G / EGFR downregulation / FCERI mediated NF-kB activation / NOTCH2 Activation and Transmission of Signal to the Nucleus / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Translesion synthesis by POLI / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Termination of translesion DNA synthesis / CLEC7A (Dectin-1) signaling / Regulation of RAS by GAPs / TNFR2 non-canonical NF-kB pathway / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / NIK-->noncanonical NF-kB signaling / Defective CFTR causes cystic fibrosis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / MAPK6/MAPK4 signaling / Degradation of GLI1 by the proteasome / Dectin-1 mediated noncanonical NF-kB signaling / Regulation of innate immune responses to cytosolic DNA / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Glycogen synthesis / Autodegradation of the E3 ubiquitin ligase COP1 / Deactivation of the beta-catenin transactivating complex / Myoclonic epilepsy of Lafora / ABC-family proteins mediated transport / Circadian Clock / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Regulation of FZD by ubiquitination / Pink/Parkin Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NFkappaB signaling pathway / Hedgehog ligand biogenesis / ER-Phagosome pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Josephin domain DUBs / InlA-mediated entry of Listeria monocytogenes into host cells / ER Quality Control Compartment (ERQC) / Neddylation / Regulation of PTEN stability and activity / Regulation of PTEN localization / Regulation of RUNX3 expression and activity / Regulation of RUNX2 expression and activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs
Ubiquitin thioesterase otulin / Ubiquitin domain / Ubiquitin conserved site / Ubiquitin / FAM105 / Ubiquitin-like domain superfamily / Ubiquitin family / Peptidase family C101 / Ubiquitin domain signature. / Ubiquitin domain profile.
Polyubiquitin-C / Ubiquitin thioesterase otulin
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsElliott, P.R. / Komander, D.
Funding supportUnited Kingdom , 1件
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)United Kingdom
CitationJournal: Cell Chem Biol / Year: 2017
Title: A Linear Diubiquitin-Based Probe for Efficient and Selective Detection of the Deubiquitinating Enzyme OTULIN.
Authors: Weber, A. / Elliott, P.R. / Pinto-Fernandez, A. / Bonham, S. / Kessler, B.M. / Komander, D. / El Oualid, F. / Krappmann, D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 7, 2017 / Release: Sep 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 27, 2017Structure modelrepositoryInitial release
1.1Nov 1, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin thioesterase otulin
B: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)48,2192
Polymers48,2192
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-10 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)101.143, 101.143, 277.916
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 31726.420 Da / Num. of mol.: 1
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, EC: 3.4.19.12
#2: Protein/peptide Polyubiquitin-C


Mass: 16492.857 Da / Num. of mol.: 1
Details: Contains an N-terminal biotin-Ahx group. DRB is derived from the non-natural amino acid ...Contains an N-terminal biotin-Ahx group. DRB is derived from the non-natural amino acid dihyrdoalanine, incorporated via chemical synthesis.
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG48

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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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 1.9-2.1 M Ammonium sulphate, 100 mM bis-tris / PH range: 6.3-6.6

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.95→54.43 Å / Num. obs: 11908 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.6
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.769 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.08 Å54.43 Å
Translation6.08 Å54.43 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.27data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZNZ
Resolution: 2.95→54.43 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.888 / SU B: 63.789 / SU ML: 0.481 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.823 / ESU R Free: 0.485 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.309 619 5.2 %RANDOM
Rwork0.223 ---
Obs0.227 11286 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.06 Å2
Baniso -1Baniso -2Baniso -3
1-3.57 Å21.78 Å20 Å2
2--3.57 Å20 Å2
3----11.57 Å2
Refinement stepCycle: LAST / Resolution: 2.95→54.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 0 0 3077
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.020.0193145
r_bond_other_d0.0030.022799
r_angle_refined_deg2.1571.9624299
r_angle_other_deg1.2236432
r_dihedral_angle_1_deg7.6255407
r_dihedral_angle_2_deg37.87624.846130
r_dihedral_angle_3_deg18.55615466
r_dihedral_angle_4_deg18.0381514
r_chiral_restr0.1220.2514
r_gen_planes_refined0.010.0213548
r_gen_planes_other0.0030.02615
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 37 -
Rwork0.418 819 -
Obs--99.77 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.40620.2350.4333.30042.12734.3671-0.0368-0.531-0.03790.1764-0.01880.20780.0685-0.24560.05560.1316-0.0240.02230.10410.00920.0165-14.115734.93625.6518
22.4943-0.15370.37151.17170.81715.1234-0.0715-0.13880.03390.30620.1137-0.30630.67270.8678-0.04220.24430.1573-0.03610.2946-0.10920.2195.299627.112619.3173
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDAuth asym-IDAuth seq-ID
11A78 - 350
22B1 - 146

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