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Yorodumi- PDB-2lxp: NMR structure of two domains in ubiquitin ligase gp78, RING and G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lxp | ||||||
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Title | NMR structure of two domains in ubiquitin ligase gp78, RING and G2BR, bound to its conjugating enzyme Ube2g | ||||||
Components |
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Keywords | LIGASE / RING domain / ubiquitin | ||||||
Function / homology | Function and homology information negative regulation of retrograde protein transport, ER to cytosol / regulation of SREBP signaling pathway / positive regulation of plant-type hypersensitive response / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / Derlin-1 retrotranslocation complex / BAT3 complex binding / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin-specific protease binding ...negative regulation of retrograde protein transport, ER to cytosol / regulation of SREBP signaling pathway / positive regulation of plant-type hypersensitive response / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / Derlin-1 retrotranslocation complex / BAT3 complex binding / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin-specific protease binding / : / ERAD pathway / non-canonical NF-kappaB signal transduction / ubiquitin conjugating enzyme activity / cellular response to interferon-beta / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / ER Quality Control Compartment (ERQC) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / lipid droplet / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein-macromolecule adaptor activity / signaling receptor activity / protein-folding chaperone binding / growth cone / ubiquitin-dependent protein catabolic process / learning or memory / neuronal cell body / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / signal transduction / protein-containing complex / ATP binding / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Das, R. / Linag, Y. / Mariano, J. / Li, J. / Huang, T. / King, A. / Weissman, A. / Ji, X. / Byrd, R. | ||||||
Citation | Journal: Embo J. / Year: 2013 Title: Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine. Authors: Das, R. / Liang, Y.H. / Mariano, J. / Li, J. / Huang, T. / King, A. / Tarasov, S.G. / Weissman, A.M. / Ji, X. / Byrd, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lxp.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2lxp.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 2lxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/2lxp ftp://data.pdbj.org/pub/pdb/validation_reports/lx/2lxp | HTTPS FTP |
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-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: 18451.062 Da / Num. of mol.: 1 / Fragment: UNP residues 2-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2G2 / Production host: Escherichia coli (E. coli) / References: UniProt: P60604, ubiquitin-protein ligase |
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#2: Protein/peptide | Mass: 3365.910 Da / Num. of mol.: 1 / Fragment: UNP residues 574-600 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMFR, RNF45 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UKV5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
#3: Protein | Mass: 6473.361 Da / Num. of mol.: 1 / Fragment: UNP residues 327-384 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMFR, RNF45 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UKV5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
#4: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.7-1 mM [U-100% 13C; U-100% 15N] gp78RING, 50 mM TRIS, 2 mM TCEP, 0.2 mM sodium azide, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 7.2 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||||||||
NMR constraints | NOE constraints total: 26 / NOE long range total count: 26 | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: Lowest Haddock Scores / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 4 Å / Maximum upper distance constraint violation: 6 Å |