+Open data
-Basic information
Entry | Database: PDB / ID: 2m9y | ||||||
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Title | Solution Structure of the Catalytic Domain of HHARI | ||||||
Components | E3 ubiquitin-protein ligase ARIH1 | ||||||
Keywords | LIGASE / HHARI / RING2 / E3 ligase / Zn-binding | ||||||
Function / homology | Function and homology information PKR/eIFalpha signaling / ubiquitin-like protein transferase activity / Lewy body / RBR-type E3 ubiquitin transferase / ubiquitin conjugating enzyme binding / RSV-host interactions / Cajal body / ubiquitin ligase complex / PKR-mediated signaling / ISG15 antiviral mechanism ...PKR/eIFalpha signaling / ubiquitin-like protein transferase activity / Lewy body / RBR-type E3 ubiquitin transferase / ubiquitin conjugating enzyme binding / RSV-host interactions / Cajal body / ubiquitin ligase complex / PKR-mediated signaling / ISG15 antiviral mechanism / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / nuclear body / protein ubiquitination / ubiquitin protein ligase binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Authors | Mercier, P. / Spratt, D.E. / Shaw, G.S. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Structure of the HHARI catalytic domain shows glimpses of a HECT E3 ligase. Authors: Spratt, D.E. / Mercier, P. / 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 | 2m9y.cif.gz | 437.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m9y.ent.gz | 364.5 KB | Display | PDB format |
PDBx/mmJSON format | 2m9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2m9y_validation.pdf.gz | 464.2 KB | Display | wwPDB validaton report |
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Full document | 2m9y_full_validation.pdf.gz | 684.6 KB | Display | |
Data in XML | 2m9y_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 2m9y_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/2m9y ftp://data.pdbj.org/pub/pdb/validation_reports/m9/2m9y | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 8439.263 Da / Num. of mol.: 1 / Fragment: Catalytic Domain (UNP residues 325-396) / Mutation: C357S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARIH1, ARI, MOP6, UBCH7BP, HUSSY-27 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL References: UniProt: Q9Y4X5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.12 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: WITH EXPLICIT SOLVENT AND FULL ELECTROSTATICS, WITH EXPLICIT SOLVENT AND FULL ELECTROSTATICS | ||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1321 / NOE intraresidue total count: 349 / NOE long range total count: 380 / NOE medium range total count: 179 / NOE sequential total count: 413 | ||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0 Å / Distance rms dev error: 0 Å |