- PDB-8fik: APOBEC3A E72A inactive mutant in complex with ATTC-hairpin DNA su... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 8fik
Title
APOBEC3A E72A inactive mutant in complex with ATTC-hairpin DNA substrate
Components
DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*TP*TP*CP*GP*AP*TP*GP*GP*G)-3')
DNA dC->dU-editing enzyme APOBEC-3A
Keywords
DNA BINDING PROTEIN/DNA / APOBEC / APOBEC3A / A3A / cancer / DNA / mutation / cytidine deaminase / hairpin DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / 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
Novel AID APOBEC clade 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / PHOSPHATE ION / DNA / DNA (> 10) / DNA dC->dU-editing enzyme APOBEC-3A Similarity search - Component
A: DNA dC->dU-editing enzyme APOBEC-3A B: DNA dC->dU-editing enzyme APOBEC-3A D: DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*TP*TP*CP*GP*AP*TP*GP*GP*G)-3') H: DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*TP*TP*CP*GP*AP*TP*GP*GP*G)-3') hetero molecules
Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
-
Details
Has ligand of interest
Y
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.55 Å3/Da / Density % sol: 51.72 % / Description: Flattened needle
Crystal grow
Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.6 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 hex phosphate (phytic acid) and 45 % pentaerythritol propoxylate (5/4 PO/OH)
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source
Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953739 Å
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi