[English] 日本語
Yorodumi- PDB-3kvf: Crystal structure of the I93M mutant of ubiquitin carboxy termina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kvf | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the I93M mutant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE/SIGNALING PROTEIN / enzyme-suicide substrate complex / cytoplasm / disease mutation / glycoprotein / hydrolase / ligase / oxidation / polymorphism / protease / thiol protease / UBL conjugation pathway / isopeptide bond / nucleus / phosphoprotein / UBL conjugation / hydrolase-hydrolase inhibitor complex / Acetylation / HYDROLASE-SIGNALING PROTEIN complex | |||||||||
Function / homology | Function and homology information axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / : / : / protein modification process => GO:0036211 / muscle cell development / neuron projection terminus / adult walking behavior / neuromuscular process ...axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / : / : / protein modification process => GO:0036211 / muscle cell development / neuron projection terminus / adult walking behavior / neuromuscular process / eating behavior / axonal transport of mitochondrion / protein deubiquitination / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of macroautophagy / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / axon cytoplasm / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / 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 / PINK1-PRKN Mediated Mitophagy / APC-Cdc20 mediated degradation of Nek2A / cytosolic ribosome / 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 / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / 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 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKBKE / negative regulation of MAP kinase activity / 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 / ubiquitin binding / 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 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / response to ischemia / Degradation of DVL / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Davies, C.W. / Maiti, T.K. / Das, C. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation. Authors: Boudreaux, D.A. / Maiti, T.K. / Davies, C.W. / Das, C. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3kvf.cif.gz | 133.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3kvf.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/3kvf ftp://data.pdbj.org/pub/pdb/validation_reports/kv/3kvf | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ifwSC 3irtC 3kw5C C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25284.836 Da / Num. of mol.: 1 / Mutation: I93M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PGP9.5, UCHL1 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: P09936, ubiquitinyl hydrolase 1, Ligases |
---|---|
#2: Protein | Mass: 8519.778 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: RPS27A, UBA52, UBA80, UBB, UBC, UBCEP1, UBCEP2, UBIQ_HUMAN Plasmid: PTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P62988, UniProt: P0CG48*PLUS |
#3: Chemical | ChemComp-GVE / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.11 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1M BICINE, 2.4M Ammonium Sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 30, 2009 / Details: mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→70.2 Å / Num. obs: 6996 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 10.5 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.856 / % possible all: 99.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IFW Resolution: 2.8→40.72 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.906 / SU B: 57.287 / SU ML: 0.476 / Cross valid method: THROUGHOUT / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 109.927 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→40.72 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.801→2.874 Å / Total num. of bins used: 20
|