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Yorodumi- PDB-2kbo: Structure, interaction, and real-time monitoring of the enzymatic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kbo | ||||||
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Title | Structure, interaction, and real-time monitoring of the enzymatic reaction of wild type APOBEC3G | ||||||
Components | DNA dC->dU-editing enzyme APOBEC-3G | ||||||
Keywords | HYDROLASE / Cytidine deaminase / HIV / APOBEC3G / Alternative splicing / Antiviral defense / Cytoplasm / Host-virus interaction / Metal-binding / Nucleus / Polymorphism / Ubl conjugation / Zinc | ||||||
Function / homology | Function and homology information apolipoprotein B mRNA editing enzyme complex / dCTP deaminase activity / cytidine deamination / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / : / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate ...apolipoprotein B mRNA editing enzyme complex / dCTP deaminase activity / cytidine deamination / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / : / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of viral process / : / retrotransposon silencing / negative regulation of viral genome replication / APOBEC3G mediated resistance to HIV-1 infection / positive regulation of defense response to virus by host / Vif-mediated degradation of APOBEC3G / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Furukawa, A. / Nagata, T. / Matsugami, A. / Habu, Y. / Sugiyama, R. / Hayashi, F. / Kobayashi, N. / Yokoyama, S. / Takaku, H. / Katahira, M. | ||||||
Citation | Journal: Embo J. / Year: 2009 Title: Structure, interaction and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G Authors: Furukawa, A. / Nagata, T. / Matsugami, A. / Habu, Y. / Sugiyama, R. / Hayashi, F. / Kobayashi, N. / Yokoyama, S. / Takaku, H. / Katahira, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kbo.cif.gz | 616.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kbo.ent.gz | 509.7 KB | Display | PDB format |
PDBx/mmJSON format | 2kbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/2kbo ftp://data.pdbj.org/pub/pdb/validation_reports/kb/2kbo | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 22926.904 Da / Num. of mol.: 1 / Fragment: UNP residues 193-384 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MDS019 / Production host: Escherichia coli (E. coli) References: UniProt: Q9HC16, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.3mM [U-100% 13C; U-100% 15N] APOBEC3G-1, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.3 mM / Component: APOBEC3G-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 30 / pH: 7.5 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1 |