+Open data
-Basic information
Entry | Database: PDB / ID: 2m65 | ||||||
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Title | NMR structure of human restriction factor APOBEC3A | ||||||
Components | Probable DNA dC->dU-editing enzyme APOBEC-3A | ||||||
Keywords | HYDROLASE / APOBEC3A / Cytidine deaminase / Antiviral defense / HOST-VIRUS INTERACTION / Zinc-binding | ||||||
Function / homology | Function and homology information mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / retrotransposon silencing ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / retrotransposon silencing / DNA demethylation / negative regulation of viral genome replication / P-body / defense response to virus / innate immune response / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Byeon, I.L. / Byeon, C. / Ahn, J. / Gronenborn, A.M. | ||||||
Citation | Journal: Nat Commun / Year: 2013 Title: NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity. Authors: Byeon, I.J. / Ahn, J. / Mitra, M. / Byeon, C.H. / Hercik, K. / Hritz, J. / Charlton, L.M. / Levin, J.G. / Gronenborn, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m65.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2m65.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 2m65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/2m65 ftp://data.pdbj.org/pub/pdb/validation_reports/m6/2m65 | 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: 24112.170 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3A / Plasmid: pET21 / Production host: Escherichia coli (E. coli) References: UniProt: P31941, 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: 13C,15N-APOBEC3A, 93% H2O/7% D2O / Solvent system: 93% H2O/7% D2O |
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Sample conditions | pH: 6.5 / Pressure: ambient / Temperature units: K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: X-PLOR NIH / Developer: Schwieters, C.D. et al. / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 512 / Conformers submitted total number: 30 |