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Yorodumi- PDB-5ohk: Crystal structure of USP30 in covalent complex with ubiquitin pro... -
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-Basic information
Entry | Database: PDB / ID: 5ohk | ||||||
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Title | Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (high resolution) | ||||||
Components |
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Keywords | HYDROLASE / Deubiquitinase / DUB / Ubiquitin / USP | ||||||
Function / homology | Function and homology information protein K6-linked deubiquitination / protein K11-linked deubiquitination / pexophagy / deubiquitinase activity / autophagy of mitochondrion / hypothalamus gonadotrophin-releasing hormone neuron development / peroxisomal membrane / negative regulation of mitophagy / female meiosis I / positive regulation of protein monoubiquitination ...protein K6-linked deubiquitination / protein K11-linked deubiquitination / pexophagy / deubiquitinase activity / autophagy of mitochondrion / hypothalamus gonadotrophin-releasing hormone neuron development / peroxisomal membrane / negative regulation of mitophagy / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / mitochondrial fusion / fat pad development / female gonad development / seminiferous tubule development / protein deubiquitination / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / 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 / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / 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 / neuron projection morphogenesis / 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) / regulation of mitochondrial membrane potential / 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 / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / Evasion by RSV of host interferon responses / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Gersch, M. / Komander, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: Mechanism and regulation of the Lys6-selective deubiquitinase USP30. Authors: Gersch, M. / Gladkova, C. / Schubert, A.F. / Michel, M.A. / Maslen, S. / Komander, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ohk.cif.gz | 92.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ohk.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ohk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/5ohk ftp://data.pdbj.org/pub/pdb/validation_reports/oh/5ohk | HTTPS FTP |
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-Related structure data
Related structure data | 5ohnC 5ohpC 2hd5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38469.422 Da / Num. of mol.: 1 Fragment: UNP residues 64-178,UNP residues 217-357,UNP residues 432-502 Mutation: construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A),construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A),construct 13 (R179G, ...Mutation: construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A),construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A),construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP30 / Plasmid: MG-26-82 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 pLacI / Strain (production host): Rosetta 2 (DE3) pLacI / References: UniProt: Q70CQ3, ubiquitinyl hydrolase 1 |
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#2: Protein | Mass: 8558.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLacI / References: UniProt: P0CG47 |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-AYE / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 10% (w/v) PEG 20000, 0.1 M sodium citrate pH 5.4, 0.2 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2016 |
Radiation | Monochromator: Double Crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→67.352 Å / Num. obs: 20131 / % possible obs: 99.18 % / Redundancy: 4.2 % / Biso Wilson estimate: 31.81 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.1701 / Rpim(I) all: 0.09162 / Net I/σ(I): 4.61 |
Reflection shell | Resolution: 2.34→2.424 Å / Redundancy: 4 % / Rmerge(I) obs: 0.7145 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 1978 / CC1/2: 0.848 / Rpim(I) all: 0.3804 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HD5 Resolution: 2.34→67.352 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→67.352 Å
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Refine LS restraints |
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LS refinement shell |
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