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Yorodumi- PDB-6hei: Structure of the catalytic domain of USP28 (insertion deleted) bo... -
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-Basic information
Entry | Database: PDB / ID: 6hei | |||||||||
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Title | Structure of the catalytic domain of USP28 (insertion deleted) bound to Ubiquitin-PA | |||||||||
Components |
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Keywords | HYDROLASE / Ubiquitin / USP / Ubiquitin-specific protease / DUB / Deubiquitinase / protease / isopeptidase / USP28 | |||||||||
Function / homology | Function and homology information protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / protein deubiquitination / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / response to ionizing radiation / female gonad development ...protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / protein deubiquitination / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / response to ionizing radiation / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / neuron projection morphogenesis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / 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 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / 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 / EGFR downregulation / 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 / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / DNA damage checkpoint signaling / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / positive regulation of protein ubiquitination / 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 / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | |||||||||
Authors | Gersch, M. / Komander, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Mol.Cell / Year: 2019 Title: Distinct USP25 and USP28 Oligomerization States Regulate Deubiquitinating Activity. Authors: Gersch, M. / Wagstaff, J.L. / Toms, A.V. / Graves, B. / Freund, S.M.V. / Komander, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hei.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hei.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 6hei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hei_validation.pdf.gz | 446.3 KB | Display | wwPDB validaton report |
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Full document | 6hei_full_validation.pdf.gz | 448.3 KB | Display | |
Data in XML | 6hei_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 6hei_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/6hei ftp://data.pdbj.org/pub/pdb/validation_reports/he/6hei | HTTPS FTP |
-Related structure data
Related structure data | 6hehC 6hejC 6hekC 6helC 6hemC 1nbfS 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: 44586.691 Da / Num. of mol.: 1 Mutation: residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLacI / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1 |
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#2: Protein | Mass: 8713.023 Da / Num. of mol.: 1 / Mutation: residue 76 replaced with PA warhead Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47 |
#3: Chemical | ChemComp-EDO / |
#4: 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: 1.97 Å3/Da / Density % sol: 37.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 22% (w/v) PEG 3350, 300 mM potassium sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→49.51 Å / Num. obs: 52145 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.057 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 4 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5114 / CC1/2: 0.69 / Rrim(I) all: 0.733 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NBF Resolution: 1.64→49.51 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→49.51 Å
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Refine LS restraints |
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LS refinement shell |
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