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Yorodumi- PDB-5e6j: Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin acti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e6j | ||||||||||||||||||
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Title | Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe | ||||||||||||||||||
Components |
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Keywords | HYDROLASE / SARS PLpro / deubiquitinating enzyme / ubiquitin / activity based probe / K48-linkage | ||||||||||||||||||
Function / homology | Function and homology information Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / hypothalamus gonadotrophin-releasing hormone neuron development / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / hypothalamus gonadotrophin-releasing hormone neuron development / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / female gonad development / seminiferous tubule development / male meiosis I / viral transcription / SARS-CoV-1 modulates host translation machinery / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / neuron projection morphogenesis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / 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 / Transferases; Transferring one-carbon groups; Methyltransferases / 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 / regulation of mitochondrial membrane potential / 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 / positive regulation of protein ubiquitination / 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 Similarity search - Function | ||||||||||||||||||
Biological species | Human SARS coronavirus Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||||||||||||||
Authors | Lima, C.D. / Bekes, M. | ||||||||||||||||||
Funding support | United States, Netherlands, 5items
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Citation | Journal: Mol. Cell / Year: 2016 Title: Recognition of Lys48-Linked Di-ubiquitin and Deubiquitinating Activities of the SARS Coronavirus Papain-like Protease. Authors: Bekes, M. / van der Heden van Noort, G.J. / Ekkebus, R. / Ovaa, H. / Huang, T.T. / Lima, C.D. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e6j.cif.gz | 196.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e6j.ent.gz | 155 KB | Display | PDB format |
PDBx/mmJSON format | 5e6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e6j_validation.pdf.gz | 484.3 KB | Display | wwPDB validaton report |
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Full document | 5e6j_full_validation.pdf.gz | 489.5 KB | Display | |
Data in XML | 5e6j_validation.xml.gz | 33 KB | Display | |
Data in CIF | 5e6j_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/5e6j ftp://data.pdbj.org/pub/pdb/validation_reports/e6/5e6j | 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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Details | Trimer confirmed by cross-linking and gel filtration |
-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 36688.527 Da / Num. of mol.: 2 / Fragment: UNP Residues 1541-1856 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human SARS coronavirus / Gene: rep, 1a-1b / Plasmid: pET28 / Details (production host): C-terminal 6xHis-tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) RIL Codon Plus References: UniProt: P0C6X7, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, RNA-directed RNA polymerase, DNA ...References: UniProt: P0C6X7, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, RNA-directed RNA polymerase, DNA helicase, RNA helicase, Transferases; Transferring one-carbon groups; Methyltransferases, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds #2: Protein | Mass: 8624.899 Da / Num. of mol.: 2 / Mutation: K48LYQ, G76AYE / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG48 #3: Protein | Mass: 8519.778 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG47 |
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-Non-polymers , 3 types, 57 molecules
#4: Chemical | ChemComp-ACT / |
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#5: Chemical | ChemComp-NI / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.1 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000 Temp details: Crystal moved to 277K 24-hour prior to mounting |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 26147 / % possible obs: 98 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.99 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.97 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MM3, 1UBQ Resolution: 2.85→49.216 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.26 / Phase error: 31.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→49.216 Å
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Refine LS restraints |
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LS refinement shell |
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