positive regulation of TORC2 signaling / protein K48-linked deubiquitination / deubiquitinase activity / protein K63-linked deubiquitination / neural crest cell differentiation / K48-linked deubiquitinase activity / protein deubiquitination / K63-linked deubiquitinase activity / negative regulation of type I interferon production / Maturation of protein E ...positive regulation of TORC2 signaling / protein K48-linked deubiquitination / deubiquitinase activity / protein K63-linked deubiquitination / neural crest cell differentiation / K48-linked deubiquitinase activity / protein deubiquitination / K63-linked deubiquitinase activity / negative regulation of type I interferon production / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / positive regulation of TORC1 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Degradation of AXIN / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity Similarity search - Function
: / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. ...: / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology
#112 - Apr 2009 Oct and Sox Transcription Factors similarity (1)
-
Assembly
Deposited unit
A: OTU domain-containing protein 5 B: Polyubiquitin-C C: OTU domain-containing protein 5 D: Polyubiquitin-C E: OTU domain-containing protein 5 F: Polyubiquitin-C G: OTU domain-containing protein 5 H: Polyubiquitin-C
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2010
Radiation
Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9786 Å / Relative weight: 1
Reflection
Resolution: 1.91→50 Å / Num. all: 75788 / Num. obs: 73969 / % possible obs: 97.6 % / Redundancy: 2 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.321 / Net I/σ(I): 14.5
Reflection shell
Resolution: 1.91→1.98 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 7278 / Rsym value: 0.321 / % possible all: 95.4
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
PHASES
phasing
REFMAC
5.5.0109
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→46.35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.345 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22721
3749
5.1 %
RANDOM
Rwork
0.18987
-
-
-
obs
0.19182
70216
97.6 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 27.269 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.2 Å2
-0.4 Å2
0.32 Å2
2-
-
-0.77 Å2
-0.31 Å2
3-
-
-
0.49 Å2
Refinement step
Cycle: LAST / Resolution: 1.91→46.35 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7820
0
0
846
8666
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.022
7969
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.109
1.94
10730
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.112
5
944
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.851
24.796
442
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.028
15.042
1433
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.151
15
51
X-RAY DIFFRACTION
r_chiral_restr
0.098
0.2
1136
X-RAY DIFFRACTION
r_gen_planes_refined
0.015
0.021
6107
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.542
1.5
4768
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.546
2
7683
X-RAY DIFFRACTION
r_scbond_it
4.042
3
3201
X-RAY DIFFRACTION
r_scangle_it
5.94
4.5
3047
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.91→1.96 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.325
283
-
Rwork
0.263
4992
-
obs
-
-
94.55 %
+
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