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Yorodumi- PDB-4uf6: UCH-L5 in complex with ubiquitin-propargyl bound to an activating... -
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-Basic information
Entry | Database: PDB / ID: 4uf6 | ||||||
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Title | UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G | ||||||
Components |
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Keywords | HYDROLASE / DEUBIQUITINATING ENZYME | ||||||
Function / homology | Function and homology information lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / positive regulation of smoothened signaling pathway / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination ...lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / positive regulation of smoothened signaling pathway / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / regulation of chromosome organization / midbrain development / endopeptidase inhibitor activity / female gonad development / proteasome binding / seminiferous tubule development / male meiosis I / protein deubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of DNA replication / regulation of embryonic development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of DNA repair / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of DNA repair / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / 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 / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / telomere maintenance / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.69 Å | ||||||
Authors | Sahtoe, D.D. / Van Dijk, W.J. / El Oualid, F. / Ekkebus, R. / Ovaa, H. / Sixma, T.K. | ||||||
Citation | Journal: Mol.Cell / Year: 2015 Title: Mechanism of Uch-L5 Activation and Inhibition by Deubad Domains in Rpn13 and Ino80G. Authors: Sahtoe, D.D. / Van Dijk, W.J. / El Oualid, F. / Ekkebus, R. / Ovaa, H. / Sixma, T.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uf6.cif.gz | 678.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uf6.ent.gz | 586.1 KB | Display | PDB format |
PDBx/mmJSON format | 4uf6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/4uf6 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/4uf6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 37734.934 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: ACTIVE SITE CYS88 COVALENTLY LINKED TO UBIQUITIN-PROPARGYL Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-NKI-3C-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q9Y5K5, ubiquitinyl hydrolase 1 #2: Protein | Mass: 8558.857 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: GLY76 OF UBIQUITIN IS REPLACED BY GLY-AYE THAT IS COVALENTLY LINKED TO THE ACTIVE SITE CYS88 OF UCH- L5 Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P0CG47 #3: Protein | Mass: 7474.066 Da / Num. of mol.: 4 Fragment: ACTIVATING FRAGMENT OF INO80G DEUBAD DOMAIN, RESIDUES 40-101 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-NKI-HIS-3C-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q6P4R8 Nonpolymer details | PROP-2-EN-1-AMINE (AYE): AYE REPLACE UBIQUITIN GLY76 | Sequence details | ISOFORM 3 GLY76 IN NATIVE UBIQUITIN IS REPLACED BY AYE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | Temperature: 277 K Details: 100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.69→47.74 Å / Num. obs: 21090 / % possible obs: 97 % / Observed criterion σ(I): 1.8 / Redundancy: 4.2 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3.69→3.98 Å / Redundancy: 4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.8 / % possible all: 90.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: STRUCTURE OF THE UCH-L5-UBIQUITIN FROM THE Resolution: 3.69→100.99 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.876 / SU B: 118.096 / SU ML: 0.739 / Cross valid method: THROUGHOUT / ESU R Free: 0.835 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 4-FOLD NCS WAS PRESENT IN THE ASYMMETRIC UNIT. LOCAL NCS RESTRAINTS WERE APPLIED IN REFMAC DURING REFINEMENT.
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.548 Å2
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Refinement step | Cycle: LAST / Resolution: 3.69→100.99 Å
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Refine LS restraints |
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