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Yorodumi- PDB-2lc3: Solution NMR structure of a helical bundle domain from human E3 l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lc3 | ||||||
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Title | Solution NMR structure of a helical bundle domain from human E3 ligase HECTD1. Northeast structural genomics consortium (NESG) target HT6305A | ||||||
Components | E3 ubiquitin-protein ligase HECTD1 | ||||||
Keywords | LIGASE / helical bundle / Structural Genomics / Northeast Structural Genomics Consortium / NESG / STRUCTURAL GENOMICS CONSORTIUM / SGC / PSI-Biology | ||||||
Function / homology | Function and homology information anatomical structure development / HECT-type E3 ubiquitin transferase / heart valve development / aorta development / ventricular septum development / protein K63-linked ubiquitination / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process ...anatomical structure development / HECT-type E3 ubiquitin transferase / heart valve development / aorta development / ventricular septum development / protein K63-linked ubiquitination / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / restrained molecular dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Lemak, A. / Yee, A. / Houliston, S. / Garcia, M. / Arrowsmith, C. / Dhe-Paganon, S. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: NMR solution structure of a helical bundle from the E3 ligase HECTD1 Authors: Lemak, A. / Yee, A. / Houliston, S. / Garcia, M. / Arrowsmith, C. / Dhe-Paganon, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lc3.cif.gz | 546.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lc3.ent.gz | 463.5 KB | Display | PDB format |
PDBx/mmJSON format | 2lc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/2lc3 ftp://data.pdbj.org/pub/pdb/validation_reports/lc/2lc3 | HTTPS FTP |
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-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: 10079.366 Da / Num. of mol.: 1 / Fragment: sequence database residues 1879-1966 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HECTD1, KIAA1131 / Production host: Escherichia coli (E. coli) References: UniProt: Q9ULT8, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM [U-13C; U-15N] protein, 10 mM TRIS, 500 mM sodium chloride, 10 uM ZnSO4, 10 mM DTT, 0.01 % NaN3, 10 mM benzamidine, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 500 / pH: 7.7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: restrained molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||||||
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 |