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Yorodumi- PDB-1cmx: STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDR... -
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-Basic information
Entry | Database: PDB / ID: 1cmx | ||||||
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Title | STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDROLASES | ||||||
Components | (PROTEIN (UBIQUITIN YUH1-UBAL)) x 2 | ||||||
Keywords | HYDROLASE / UBIQUITIN HYDROLASE / UBIQUITIN / DEUBIQUITINATING ENZYME / CYSTEINE PROTEASE / ENZYME SPECIFICITY | ||||||
Function / homology | Function and homology information UCH proteinases / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / : / : / ubiquitin recycling / protein modification process => GO:0036211 / Neddylation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits ...UCH proteinases / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / : / : / ubiquitin recycling / protein modification process => GO:0036211 / Neddylation / 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) / cytosolic ribosome / 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 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / 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 / Dectin-1 mediated noncanonical NF-kB signaling Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å | ||||||
Authors | Johnston, S.C. / Riddle, S.M. / Cohen, R.E. / Hill, C.P. | ||||||
Citation | 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. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cmx.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cmx.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 1cmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cmx_validation.pdf.gz | 457.1 KB | Display | wwPDB validaton report |
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Full document | 1cmx_full_validation.pdf.gz | 470.6 KB | Display | |
Data in XML | 1cmx_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 1cmx_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/1cmx ftp://data.pdbj.org/pub/pdb/validation_reports/cm/1cmx | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 26276.117 Da / Num. of mol.: 2 / Fragment: ALL / Source method: obtained synthetically Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN THE CYTOPLASM OF PLASMID P-1A2/TRPYUH1-1 OF SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). THE ...Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN THE CYTOPLASM OF PLASMID P-1A2/TRPYUH1-1 OF SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). THE EXPRESSION SYSTEM WAS ESCHERICHIA COLI, STRAIN MM294, PLASMID P-1A2/TRPYUH1-1. References: UniProt: P35127, EC: 3.1.2.15 #2: Protein | Mass: 8560.831 Da / Num. of mol.: 2 / Fragment: ALL / Source method: obtained synthetically Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN THE CYTOPLASM OF PLASMID P-1A2/TRPYUH1-1 OF SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). THE ...Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN THE CYTOPLASM OF PLASMID P-1A2/TRPYUH1-1 OF SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). THE EXPRESSION SYSTEM WAS ESCHERICHIA COLI, STRAIN MM294, PLASMID P-1A2/TRPYUH1-1. References: UniProt: P02248, UniProt: P0CG48*PLUS, EC: 3.1.2.15 #3: Water | ChemComp-HOH / | Compound details | TER GLY: MODIFIED TO ALDEHYDE GLY: MODIFIED TO ALDEHYDE | |
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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: 2.01 Å3/Da / Density % sol: 40 % | |||||||||||||||
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Crystal grow | pH: 4.5 / Details: 16% PEG 6000 0.1 M SODIUM ACETATE PH 4.4, pH 4.5 | |||||||||||||||
Crystal | *PLUS Density % sol: 40 % | |||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Date: Feb 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 26106 / % possible obs: 99 % / Redundancy: 4.3 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.037 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.202 / % possible all: 96.2 |
Reflection | *PLUS Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 96 % / Rmerge(I) obs: 0.202 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.25→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.35 Å / Total num. of bins used: 10 /
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Xplor file | Serial no: 1 / Param file: PARHCSDX_UBAL.PRO / Topol file: TOPHCSDX_UBAL.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 98 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.248 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.43 / Rfactor Rwork: 0.349 / Rfactor obs: 0.349 |