+Open data
-Basic information
Entry | Database: PDB / ID: 1fxt | ||||||
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Title | STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER COMPLEX | ||||||
Components |
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Keywords | LIGASE / Model of the interaction between yeast Ubc1 and Ubiquitin after the formation of a covalent thiolester | ||||||
Function / homology | Function and homology information Synthesis of active ubiquitin: roles of E1 and E2 enzymes / : / : / vesicle organization / protein modification process => GO:0036211 / E2 ubiquitin-conjugating enzyme / proteasome binding / Peptide chain elongation / Selenocysteine synthesis / ubiquitin conjugating enzyme activity ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / : / : / vesicle organization / protein modification process => GO:0036211 / E2 ubiquitin-conjugating enzyme / proteasome binding / Peptide chain elongation / Selenocysteine synthesis / ubiquitin conjugating enzyme activity / Formation of a pool of free 40S subunits / Antigen processing: Ubiquitination & Proteasome degradation / 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 / ERAD pathway / 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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / 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 / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / 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 / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / 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 | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / Dynamic docking between Ubc1, Ub System covalently bound, minimized | ||||||
Authors | Hamilton, K.S. / Shaw, G.S. / Williams, R.S. / Huzil, J.T. / McKenna, S. / Ptak, C. / Glover, M. / Ellison, M.J. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail. Authors: Hamilton, K.S. / Ellison, M.J. / Barber, K.R. / Williams, R.S. / Huzil, J.T. / McKenna, S. / Ptak, C. / Glover, M. / Shaw, G.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fxt.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fxt.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 1fxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fxt_validation.pdf.gz | 252.7 KB | Display | wwPDB validaton report |
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Full document | 1fxt_full_validation.pdf.gz | 252.4 KB | Display | |
Data in XML | 1fxt_validation.xml.gz | 6 KB | Display | |
Data in CIF | 1fxt_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/1fxt ftp://data.pdbj.org/pub/pdb/validation_reports/fx/1fxt | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16697.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P21734, ubiquitin-protein ligase |
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#2: Protein | Mass: 8576.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3A-HUB / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: enhanced 1H-15N HSQC |
NMR details | Text: Spectra of thiolester formation were acquired every 10 minutes during the first 60 minutes of reaction time until a stable level of covalent complex was formed |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 450mM NaCl / pH: 7.5 / Pressure: ambient / Temperature: 30 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: Dynamic docking between Ubc1, Ub System covalently bound, minimized Software ordinal: 1 | ||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||
NMR ensemble | Conformers calculated total number: 1 / Conformers submitted total number: 1 |