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- PDB-8fij: Wild type APOBEC3A in complex with TT(FdZ)-hairpin inhibitor (cry... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fij | ||||||
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Title | Wild type APOBEC3A in complex with TT(FdZ)-hairpin inhibitor (crystal form 2) | ||||||
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![]() | DNA BINDING PROTEIN / APOBEC / APOBEC3A / A3A / cancer / DNA / mutation / cytidine deaminase / hairpin DNA inhibitor | ||||||
Function / homology | ![]() mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / positive regulation of gene expression via chromosomal CpG island demethylation / retrotransposon silencing / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harjes, S. / Jameson, G.B. / Harjes, E. / Filichev, V.V. / Kurup, H.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: DNA-based inhibitors restrict mutagenic activity of APOBEC3 in cells Authors: Harjes, S. / Kurup, H.M. / Filichev, V. / Harjes, E. / Jameson, G.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.5 KB | Display | ![]() |
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PDB format | ![]() | 133.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8fiiC ![]() 8fikC ![]() 8filC ![]() 8fimC ![]() 5kegS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 10 - 196 / Label seq-ID: 10 - 196
NCS ensembles : (Details: Global NCS restraints between domains: 1 2) NCS oper:
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Components
#1: Protein | Mass: 23041.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P31941, single-stranded DNA cytosine deaminase #2: DNA chain | Mass: 3649.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.65 % / Description: Flattened needle |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop Details: A3A-E72A (50 mM MES pH 6.0, 100 mM NaCl, 1 mM TCEP, 0.2 mM EDTA) was mixed with oligonucleotides (10 mM Tris/HCl pH 7.9, 1 mM EDTA) at 0.85 mM and 1.7 mM respectively. Dilution was done with ...Details: A3A-E72A (50 mM MES pH 6.0, 100 mM NaCl, 1 mM TCEP, 0.2 mM EDTA) was mixed with oligonucleotides (10 mM Tris/HCl pH 7.9, 1 mM EDTA) at 0.85 mM and 1.7 mM respectively. Dilution was done with protein buffer. The mixture was added to crystallization liquid 1 to 1 and the mixture was pipetted on siliconized glass disks and sealed on top of a reservoir of crystallization liquid for hanging drop crystallization at 12 degrees Celsius. The crystallization liquid has the following composition: 100 mM Bicine at pH 6.6, 200 mM NaCl, 20 mM putrescine, 1 mM TCEP, 1 mM inositol hexaphosphate (phytic acid) and 45 % pentaerythritol propoxylate (5/4 PO/OH) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2021 / Details: 1 vertical and 2 horizontal focussing mirrors |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953739 Å / Relative weight: 1 |
Reflection | Resolution: 2.799→48.291 Å / Num. obs: 11861 / % possible obs: 97.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 57 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.118 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.157 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1629 / CC1/2: 0.466 / Rpim(I) all: 0.735 / % possible all: 92.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KEG Resolution: 2.799→48.291 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.834 / WRfactor Rfree: 0.313 / WRfactor Rwork: 0.251 / SU B: 67.886 / SU ML: 0.581 / Average fsc free: 0.7681 / Average fsc work: 0.7885 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.975 Å2
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Refinement step | Cycle: LAST / Resolution: 2.799→48.291 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Rms dev Biso : 5.13109 Å2 / Rms dev position: 0.27737 Å / Weight Biso : 0.5 / Weight position: 0.05
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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