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Yorodumi- PDB-2ljy: Haddock model structure of the N-terminal domain dimer of HPV16 E6 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ljy | ||||||
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Title | Haddock model structure of the N-terminal domain dimer of HPV16 E6 | ||||||
Components | Protein E6 | ||||||
Keywords | METAL BINDING PROTEIN | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / PDZ domain binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / DNA-templated transcription ...symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / PDZ domain binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Human papillomavirus | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Zanier, K. / Muhamed Sidi, A. / Boulade-Ladame, C. / Rybin, V. / Chappelle, A. / Atkinson, A. / Kieffer, B. / Trave, G. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Solution Structure Analysis of the HPV16 E6 Oncoprotein Reveals a Self-Association Mechanism Required for E6-Mediated Degradation of p53. Authors: Zanier, K. / Ould M'hamed Ould Sidi, A. / Boulade-Ladame, C. / Rybin, V. / Chappelle, A. / Atkinson, A. / Kieffer, B. / Trave, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ljy.cif.gz | 914.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ljy.ent.gz | 762.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ljy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/2ljy ftp://data.pdbj.org/pub/pdb/validation_reports/lj/2ljy | HTTPS FTP |
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-Related structure data
Related structure data | 2ljxC 2ljzC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10138.669 Da / Num. of mol.: 2 / Fragment: Zinc finger containing residues 7-86 / Mutation: C80S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human papillomavirus / Strain: type 16 / Gene: E6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03126 #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: NMR data driven model structure of the N-terminal domain dimer of HPV16 E6 calculated using Haddock | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The dimer structures were calculated using Ambiguous Interaction restrains, unambiguous inter-molecular NOE-derived distance restraints and dihedral angles. |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 50 mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 296 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 | Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 37 / Protein psi angle constraints total count: 37 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 1.07 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 4.23 ° / Maximum upper distance constraint violation: 1 Å / Torsion angle constraint violation method: xplor | ||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.093 Å / Distance rms dev error: 0.072 Å |