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Yorodumi- PDB-3znh: Crimean Congo Hemorrhagic Fever Virus OTU domain in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 3znh | ||||||
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Title | Crimean Congo Hemorrhagic Fever Virus OTU domain in complex with ubiquitin-propargyl. | ||||||
Components |
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Keywords | HYDROLASE/SIGNALING PROTEIN / HYDROLASE-SIGNALING PROTEIN COMPLEX / DEUBIQUITINASE | ||||||
Function / homology | Function and homology information RNA-templated viral transcription / negative stranded viral RNA replication / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I ...RNA-templated viral transcription / negative stranded viral RNA replication / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / 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 / endoplasmic reticulum unfolded protein response / 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 / 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 / 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 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway Similarity search - Function | ||||||
Biological species | CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ekkebus, R. / vanKasteren, S.I. / Kulathu, Y. / Scholten, A. / Berlin, I. / deJong, A. / Goerdayal, G. / Neefjes, J. / Heck, A.J.R. / Komander, D. / Ovaa, H. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: On Terminal Alkynes that Can React with Active-Site Cysteine Nucleophiles in Proteases. Authors: Ekkebus, R. / Van Kasteren, S.I. / Kulathu, Y. / Scholten, A. / Berlin, I. / Geurink, P.P. / De Jong, A. / Goerdayal, G. / Neefjes, J. / Heck, A.J.R. / Komander, D. / Ovaa, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3znh.cif.gz | 60 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3znh.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 3znh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3znh_validation.pdf.gz | 427.2 KB | Display | wwPDB validaton report |
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Full document | 3znh_full_validation.pdf.gz | 428.8 KB | Display | |
Data in XML | 3znh_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 3znh_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/3znh ftp://data.pdbj.org/pub/pdb/validation_reports/zn/3znh | HTTPS FTP |
-Related structure data
Related structure data | 3phwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20857.414 Da / Num. of mol.: 1 / Fragment: OTU DOMAIN, RESIDUES 1-183 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS / Strain: IBAR10200 / Description: DNA GENERATED BY GENE SYNTHESIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA2 PLACI / References: UniProt: Q6TQR6, ubiquitinyl hydrolase 1 |
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#2: Protein | Mass: 8558.857 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically / Details: GLY76 IS REPLACED WITH A PROPARGYL GROUP / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P0CG47 |
#3: Water | ChemComp-HOH / |
Nonpolymer details | ALLYLAMINE (AYE): THIS IS THE PRODUCT OF COVALENT MODIFICATION FROM PROPARGYL UBIQUITIN WITH A CYS. ...ALLYLAMINE |
Sequence details | RESIDUES 1-183 RESIDUE 76 IS REPLACED WITH A PROPARGYL MOIETY, WHICH FORMS A QUATERNARY VINYL ...RESIDUES 1-183 RESIDUE 76 IS REPLACED WITH A PROPARGYL MOIETY, WHICH FORMS A QUATERNARY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 20-30% PEG 8000, 100 MM NA CACODYLATE PH 6.5, 100 MM MG ACETATE, AND 2% N-OCTYL-BETA-D-GLUCOSIDE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→53.12 Å / Num. obs: 16479 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.6 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PHW Resolution: 2.3→126.48 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.793 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. COVALENT LINKS BETWEEN MOLECULE B GLY75,ETHANAMINE76 AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. COVALENT LINKS BETWEEN MOLECULE B GLY75,ETHANAMINE76 AND MOLECULE A CYS40 HAVE BEEN REFINED IN REFMAC. DISORDERED RESIDUES WERE MODELLED WITH SIDE CHAINS REMOVED OR MUTATED TO ALA.
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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: 33.362 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→126.48 Å
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Refine LS restraints |
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