+Open data
-Basic information
Entry | Database: PDB / ID: 2lvn | ||||||
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Title | Structure of the gp78 CUE domain | ||||||
Components | E3 ubiquitin-protein ligase AMFR | ||||||
Keywords | LIGASE / CUE domain | ||||||
Function / homology | Function and homology information regulation of SREBP signaling pathway / endoplasmic reticulum mannose trimming / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / endoplasmic reticulum quality control compartment / Derlin-1 retrotranslocation complex / BAT3 complex binding / non-canonical NF-kappaB signal transduction / ubiquitin-ubiquitin ligase activity / ubiquitin-specific protease binding ...regulation of SREBP signaling pathway / endoplasmic reticulum mannose trimming / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / endoplasmic reticulum quality control compartment / Derlin-1 retrotranslocation complex / BAT3 complex binding / non-canonical NF-kappaB signal transduction / ubiquitin-ubiquitin ligase activity / ubiquitin-specific protease binding / protein autoubiquitination / protein K48-linked ubiquitination / ERAD pathway / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / ER Quality Control Compartment (ERQC) / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / signaling receptor activity / protein-macromolecule adaptor 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 / signal transduction / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Liu, S. / Chen, Y. / Huang, T. / Tarasov, S.G. / King, A. / Li, J. / Weissman, A.M. / Byrd, R.A. / Das, R. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Promiscuous Interactions of gp78 E3 Ligase CUE Domain with Polyubiquitin Chains. Authors: Liu, S. / Chen, Y. / Li, J. / Huang, T. / Tarasov, S. / King, A. / Weissman, A.M. / Byrd, R.A. / Das, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lvn.cif.gz | 329.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lvn.ent.gz | 275.6 KB | Display | PDB format |
PDBx/mmJSON format | 2lvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lvn_validation.pdf.gz | 395 KB | Display | wwPDB validaton report |
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Full document | 2lvn_full_validation.pdf.gz | 501 KB | Display | |
Data in XML | 2lvn_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 2lvn_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/2lvn ftp://data.pdbj.org/pub/pdb/validation_reports/lv/2lvn | HTTPS FTP |
-Related structure data
Related structure data | 2lvoC 2lvpC 2lvqC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 5966.752 Da / Num. of mol.: 1 / Fragment: CUE domain residues 453-504 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) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR / Details: 1H, 13C, 15N assignments of gp78 CUE domain | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 50 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||
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Sample |
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Sample conditions | 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 / Details: FINAL STEP IN WATER | ||||||||||||||||||
NMR constraints | NOE constraints total: 1189 / NOE intraresidue total count: 282 / NOE long range total count: 102 / NOE medium range total count: 634 / NOE sequential total count: 171 / Protein phi angle constraints total count: 48 / Protein psi angle constraints total count: 49 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 1.8 Å / Maximum upper distance constraint violation: 6 Å | ||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0 Å |