+Open data
-Basic information
Entry | Database: PDB / ID: 1xd3 | |||||||||
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Title | Crystal structure of UCHL3-UbVME complex | |||||||||
Components |
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Keywords | HYDROLASE / Enzyme-Ligand complex / active site crossover loop | |||||||||
Function / homology | Function and homology information : / : / protein modification process => GO:0036211 / deNEDDylase activity / 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 ...: / : / protein modification process => GO:0036211 / deNEDDylase activity / 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 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / cytosolic ribosome / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / post-translational protein modification / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / InlB-mediated entry of Listeria monocytogenes into host cell / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||
Authors | Misaghi, S. / Galardy, P.J. / Meester, W.J.N. / Ovaa, H. / Ploegh, H.L. / Gaudet, R. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structure of the Ubiquitin Hydrolase UCH-L3 Complexed with a Suicide Substrate Authors: Misaghi, S. / Galardy, P.J. / Meester, W.J.N. / Ovaa, H. / Ploegh, H.L. / Gaudet, R. #1: Journal: Chem.Biol. / Year: 2002 Title: Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family Authors: Borodovsky, A. / Ovaa, H. / Kolli, N. / Gan-Erdene, T. / Wilkinson, K.D. / Ploegh, H.L. / Kessler, B.M. #2: Journal: Embo J. / Year: 2001 Title: A novel active site-directed probe specific for deubiquitinating enzymes reveals proteasome association of USP14 Authors: Borodovsky, A. / Kessler, B.M. / Casagrande, R. / Overkleeft, H.S. / Wilkinson, K.D. / Ploegh, H.L. #3: Journal: Embo J. / Year: 1997 Title: Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution Authors: Johnston, S.C. / Larsen, C.N. / Cook, W.J. / Wilkinson, K.D. / Hill, C.P. #4: Journal: Embo J. / Year: 1999 Title: Structural basis for the specificity of ubiquitin C-terminal hydrolases Authors: Johnston, S.C. / Riddle, S.M. / Cohen, R.E. / Hill, C.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xd3.cif.gz | 167 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xd3.ent.gz | 129.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xd3_validation.pdf.gz | 458.5 KB | Display | wwPDB validaton report |
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Full document | 1xd3_full_validation.pdf.gz | 463.2 KB | Display | |
Data in XML | 1xd3_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 1xd3_validation.cif.gz | 57.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/1xd3 ftp://data.pdbj.org/pub/pdb/validation_reports/xd/1xd3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26213.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P15374, ubiquitinyl hydrolase 1 #2: Protein | Mass: 8519.778 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTYB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P62988, UniProt: P0CG48*PLUS #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9779 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2004 |
Radiation | Monochromator: Si III monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9779 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→23.76 Å / Num. all: 95726 / Num. obs: 93859 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 16 Å2 / Limit h max: 31 / Limit h min: -30 / Limit k max: 34 / Limit k min: -30 / Limit l max: 46 / Limit l min: 0 / Observed criterion F max: 662233.47 / Observed criterion F min: 0.32 / Rsym value: 0.056 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 9379 / Rsym value: 0.467 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UCH, PDB ENTRY 1UBQ Resolution: 1.45→23.76 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 50.6665 Å2 / ksol: 0.346865 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.52 Å2 / Biso mean: 19.32 Å2 / Biso min: 5.78 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.45→23.76 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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