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Yorodumi- PDB-2j7q: Crystal structure of the ubiquitin-specific protease encoded by m... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 2j7q | |||||||||
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| Title | Crystal structure of the ubiquitin-specific protease encoded by murine cytomegalovirus tegument protein M48 in complex with a ubquitin-based suicide substrate | |||||||||
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Keywords | HYDROLASE / HERPESVIRIDAE / NUCLEAR PROTEIN / COVALENT ENZYME-LIGAND COMPLEX / DEUBIQUITINATING ENZYME / PAPAIN-LIKE FOLD / CYSTEINE PROTEASE | |||||||||
| Function / homology | Function and homology information: / : / protein modification process => GO:0036211 / : / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency ...: / : / protein modification process => GO:0036211 / : / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / 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 / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / cytosolic ribosome / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ubiquitin-dependent degradation of Cyclin D / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Fanconi Anemia Pathway / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulation of FGFR3 signaling / Peroxisomal protein import / TNFR2 non-canonical NF-kB pathway / Deactivation of the beta-catenin transactivating complex / Stabilization of p53 / Assembly of the pre-replicative complex / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Vpu mediated degradation of CD4 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Cdc20:Phospho-APC/C mediated degradation of Cyclin A Similarity search - Function | |||||||||
| Biological species | MURINE CYTOMEGALOVIRUS (Murine cytomegalovirus) HOMO SAPIENS (human) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | |||||||||
Authors | Schlieker, C. / Weihofen, W.A. / Frijns, E. / Kattenhorn, L.M. / Gaudet, R. / Ploegh, H.L. | |||||||||
Citation | Journal: Mol.Cell / Year: 2007Title: Structure of a Herpesvirus-Encoded Cysteine Protease Reveals a Unique Class of Deubiquitinating Enzymes Authors: Schlieker, C. / Weihofen, W.A. / Frijns, E. / Kattenhorn, L.M. / Gaudet, R. / Ploegh, H.L. | |||||||||
| History |
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| Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2j7q.cif.gz | 152.2 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2j7q.ent.gz | 118.8 KB | Display | PDB format |
| PDBx/mmJSON format | 2j7q.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/2j7q ftp://data.pdbj.org/pub/pdb/validation_reports/j7/2j7q | HTTPS FTP |
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-Related structure data
| Related structure data | |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-MCMV TEGUMENT PROTEIN M48 ENCODED UBIQUITIN- SPECIFIC PROTEASE, ... , 2 types, 2 molecules AC
| #1: Protein | Mass: 25677.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DEUBIQUITINATING MODULE OF MURINE CYTOMEGALOVIRUS TEGUMENT PROTEIN M48. ACTIVE SITE CYSTEINE 23 IS COVALENTLY LINKED TO THE FORMER VINYLMETHYLESTER MOIETY OF THE SUICIDE SUBSTATE UBVME Source: (gene. exp.) MURINE CYTOMEGALOVIRUS (Murine cytomegalovirus)Strain: MCMV STRAIN SMITH / Plasmid: PET28 (NOVAGEN) / Production host: ![]() |
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| #3: Protein | Mass: 25686.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DEUBIQUITINATING MODULE OF MURINE CYTOMEGALOVIRUS TEGUMENT PROTEIN M48. ACTIVE SITE CYSTEINE 23 IS COVALENTLY LINKED TO THE FORMER VINYLMETHYLESTER MOIETY OF THE SUICIDE SUBSTATE UBVME Source: (gene. exp.) MURINE CYTOMEGALOVIRUS (Murine cytomegalovirus)Strain: MCMV STRAIN SMITH / Plasmid: PET28 (NOVAGEN) / Production host: ![]() |
-Protein , 1 types, 2 molecules BD
| #2: Protein | Mass: 8519.778 Da / Num. of mol.: 2 Fragment: UBIQUITIN FUSED TO VINYLMETHYLESTER, UBVME, RESIDUES 1-75 Source method: isolated from a genetically manipulated source Details: THE C-TERMINAL GLY 76 IS REPLACED BY THE VINYLMETHYLESTER MOIETY Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTYB (NEW ENGLAND BIOLABS) / Production host: ![]() |
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-Non-polymers , 5 types, 714 molecules 








| #4: Chemical | | #5: Chemical | #6: Chemical | ChemComp-PG4 / | #7: Chemical | ChemComp-GOL / | #8: 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: 1.95 Å3/Da / Density % sol: 36.49 % |
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| Crystal grow | pH: 7.5 / Details: 200 MM MAGNESIUM FORMATE, 14% PEG 3350, pH 7.50 |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9797 |
| Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 31, 2006 |
| Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
| Reflection | Resolution: 1.8→50 Å / Num. obs: 52323 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.3 |
| Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.5 / % possible all: 84.2 |
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Processing
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| Refinement | Method to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.84 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 10.21 Å2
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| Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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| Refine LS restraints |
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About Yorodumi



MURINE CYTOMEGALOVIRUS (Murine cytomegalovirus)
HOMO SAPIENS (human)
X-RAY DIFFRACTION
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