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Yorodumi- PDB-4oct: Crystal structure of human ALKBH5 crystallized in the presence of... -
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-Basic information
Entry | Database: PDB / ID: 4oct | ||||||
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Title | Crystal structure of human ALKBH5 crystallized in the presence of Mn^{2+} and 2-oxoglutarate | ||||||
Components | RNA demethylase ALKBH5 | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / Structural Genomics Consortium / SGC / RNA demethylase | ||||||
Function / homology | Function and homology information gamma-delta T cell proliferation / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of mRNA export from nucleus / oxidative RNA demethylase activity / regulation of mRNA processing / paraspeckles / non-membrane-bounded organelle assembly / 2-oxoglutarate-dependent dioxygenase activity ...gamma-delta T cell proliferation / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of mRNA export from nucleus / oxidative RNA demethylase activity / regulation of mRNA processing / paraspeckles / non-membrane-bounded organelle assembly / 2-oxoglutarate-dependent dioxygenase activity / mRNA destabilization / mRNA export from nucleus / molecular condensate scaffold activity / mRNA processing / regulation of translation / spermatogenesis / cell differentiation / response to hypoxia / nuclear speck / Golgi apparatus / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / direct placement / Resolution: 2.28 Å | ||||||
Authors | Tempel, W. / Chao, X. / Liu, K. / Dong, A. / Cerovina, T. / He, H. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation. Authors: Xu, C. / Liu, K. / Tempel, W. / Demetriades, M. / Aik, W. / Schofield, C.J. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oct.cif.gz | 179.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oct.ent.gz | 141.5 KB | Display | PDB format |
PDBx/mmJSON format | 4oct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oct_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
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Full document | 4oct_full_validation.pdf.gz | 451.7 KB | Display | |
Data in XML | 4oct_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 4oct_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/4oct ftp://data.pdbj.org/pub/pdb/validation_reports/oc/4oct | HTTPS FTP |
-Related structure data
Related structure data | 4o61SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 77 - 293 / Label seq-ID: 5 - 221
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-Components
#1: Protein | Mass: 25339.010 Da / Num. of mol.: 2 / Fragment: UNP residues 74-294 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH5, ABH5, OFOXD1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 References: UniProt: Q6P6C2, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-UNX / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 42.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 0.005 M of each manganous sulfate and 2-oxyglutarate were added to the protein stock solution. Reservoir: 20% PEG-3350, 0.2 M diammonium phosphate, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å | ||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 23, 2013 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.28→38.47 Å / Num. obs: 18808 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 13.3 | ||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.011 / Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: direct placement Starting model: related to pdb entry 4O61 Resolution: 2.28→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.2464 / WRfactor Rwork: 0.202 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.686 / SU B: 27.978 / SU ML: 0.305 / SU R Cruickshank DPI: 0.4723 / SU Rfree: 0.2846 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.472 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: PDB entry 2IUW aided in the interpretation of the manganese cation binding site. Coot was used for interactive model adjustments. Molprobity was used for validation of model geometry.
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.63 Å2 / Biso mean: 45.2232 Å2 / Biso min: 7.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 12076 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.28→2.339 Å / Total num. of bins used: 20
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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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