Crystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin vinyl methyl ester
Components
Ubiquitin
Ubiquitin carboxyl-hydrolase
Keywords
Hydrolase/Signaling Protein / helix-beta-helix sandwich / protein-protein complex / deubiquitination / ubiquitin c-terminal hydrolase / cytosol / Hydrolase-Signaling Protein complex
Function / homology
Function and homology information
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 / IRAK1 recruits IKK complex ...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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / 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 / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Termination of translesion DNA synthesis / Defective CFTR causes cystic fibrosis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / Stabilization of p53 / EGFR downregulation / Negative regulation of NOTCH4 signaling / Negative regulation of FGFR1 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Vif-mediated degradation of APOBEC3G Similarity search - Function
Method to determine structure: SAD / Resolution: 1.701→27.88 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.4 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2114
3133
5.03 %
random
Rwork
0.1744
-
-
-
obs
0.1763
62257
88.35 %
-
all
-
70466
-
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.701→27.88 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4619
0
25
346
4990
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.017
4767
X-RAY DIFFRACTION
f_angle_d
1.753
6451
X-RAY DIFFRACTION
f_dihedral_angle_d
15.647
1787
X-RAY DIFFRACTION
f_chiral_restr
0.122
736
X-RAY DIFFRACTION
f_plane_restr
0.008
830
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.7006-1.7272
0.293
59
0.276
1235
X-RAY DIFFRACTION
41
1.7272-1.7555
0.3321
75
0.2456
1431
X-RAY DIFFRACTION
47
1.7555-1.7858
0.2836
66
0.2369
1666
X-RAY DIFFRACTION
54
1.7858-1.8183
0.2436
87
0.2427
1839
X-RAY DIFFRACTION
61
1.8183-1.8532
0.3021
128
0.2363
2193
X-RAY DIFFRACTION
72
1.8532-1.891
0.3034
112
0.242
2474
X-RAY DIFFRACTION
82
1.891-1.9321
0.2539
157
0.234
2771
X-RAY DIFFRACTION
92
1.9321-1.9771
0.2652
162
0.2091
2857
X-RAY DIFFRACTION
96
1.9771-2.0265
0.2355
178
0.1948
2990
X-RAY DIFFRACTION
99
2.0265-2.0813
0.242
163
0.1845
2976
X-RAY DIFFRACTION
99
2.0813-2.1425
0.2418
151
0.1861
3088
X-RAY DIFFRACTION
100
2.1425-2.2116
0.2246
177
0.1781
2992
X-RAY DIFFRACTION
100
2.2116-2.2906
0.235
148
0.1762
3035
X-RAY DIFFRACTION
100
2.2906-2.3823
0.2402
158
0.1818
3057
X-RAY DIFFRACTION
100
2.3823-2.4907
0.2417
172
0.1816
3019
X-RAY DIFFRACTION
100
2.4907-2.6219
0.2445
167
0.1903
3028
X-RAY DIFFRACTION
100
2.6219-2.786
0.2463
169
0.1934
3056
X-RAY DIFFRACTION
100
2.786-3.0009
0.2099
170
0.19
3009
X-RAY DIFFRACTION
100
3.0009-3.3025
0.2155
146
0.1763
3087
X-RAY DIFFRACTION
100
3.3025-3.7793
0.1785
150
0.1444
3070
X-RAY DIFFRACTION
100
3.7793-4.7577
0.1586
171
0.1277
3080
X-RAY DIFFRACTION
100
4.7577-27.8832
0.1667
167
0.1633
3171
X-RAY DIFFRACTION
100
Refinement TLS params.
Method: refined / Origin x: 35.4692 Å / Origin y: 51.0532 Å / Origin z: 17.3875 Å
11
12
13
21
22
23
31
32
33
T
0.2773 Å2
0.0143 Å2
0.0083 Å2
-
0.2452 Å2
0.008 Å2
-
-
0.264 Å2
L
0.7776 °2
-0.2111 °2
1.1152 °2
-
0.0699 °2
-0.4289 °2
-
-
1.7801 °2
S
0.0156 Å °
0.1582 Å °
0.0021 Å °
-0.023 Å °
-0.0525 Å °
-0.0208 Å °
-0.0073 Å °
0.233 Å °
0.0413 Å °
Refinement TLS group
Selection details: all
+
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