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Yorodumi- PDB-4ie7: Crystal structure of the human fat mass and obesity associated pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ie7 | ||||||
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Title | Crystal structure of the human fat mass and obesity associated protein (FTO) in complex with citrate and rhein (RHN) | ||||||
Components | Alpha-ketoglutarate-dependent dioxygenase FTO | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / double-stranded beta helix / jelly-roll motif / oxidoreductase / dioxygenase / nucleic acid demethylase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information regulation of white fat cell proliferation / tRNA demethylase activity / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of respiratory system process / regulation of lipid storage / : / regulation of brown fat cell differentiation / : ...regulation of white fat cell proliferation / tRNA demethylase activity / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of respiratory system process / regulation of lipid storage / : / regulation of brown fat cell differentiation / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / 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 / DNA alkylation repair / oxidative demethylation / DNA demethylation / temperature homeostasis / mRNA destabilization / regulation of multicellular organism growth / adipose tissue development / ferrous iron binding / transferase activity / nuclear speck / intracellular membrane-bounded organelle / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6004 Å | ||||||
Authors | Aik, W.S. / McDonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Structural basis for inhibition of the fat mass and obesity associated protein (FTO) Authors: Aik, W.S. / Demetriades, M. / Hamdan, M.K.K. / Bagg, E.A.L. / Yeoh, K.K. / Lejeune, C. / Zhang, Z. / McDonough, M.A. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ie7.cif.gz | 193.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ie7.ent.gz | 153.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ie7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/4ie7 ftp://data.pdbj.org/pub/pdb/validation_reports/ie/4ie7 | HTTPS FTP |
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-Related structure data
Related structure data | 4idzC 4ie0C 4ie4C 4ie5C 4ie6C 3lfmS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56823.047 Da / Num. of mol.: 1 / Fragment: UNP residues 32-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTO, KIAA1752 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9C0B1, 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 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-RHN / |
#4: Chemical | ChemComp-FLC / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.69 % / Mosaicity: 0.333 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 11.5% PEG 3350, 100mM trisodium citrate pH5.6, 4% tert-butanol, 1mM ZnSO4, 2mM RHN, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. all: 19686 / Num. obs: 19675 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 74.65 Å2 / Rmerge(I) obs: 0.098 / Χ2: 1.041 / Net I/σ(I): 13.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3LFM Resolution: 2.6004→49.8609 Å / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Isotropic
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Displacement parameters | Biso max: 160.02 Å2 / Biso mean: 79.1727 Å2 / Biso min: 37.44 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6004→49.8609 Å
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Refine LS restraints |
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LS refinement shell |
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