+Open data
-Basic information
Entry | Database: PDB / ID: 5zmd | |||||||||
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Title | Crystal structure of FTO in complex with m6dA modified ssDNA | |||||||||
Components |
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Keywords | OXIDOREDUCTASE/DNA / RNA demetheylase FTO / m6A / substrate preference / RNA BINDING PROTEIN / OXIDOREDUCTASE-DNA 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 / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity ...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 / snRNA processing / 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 / RNA repair / DNA alkylation repair / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) DNA launch vector pDE-GFP2 (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Zhang, X. / Wei, L.H. / Luo, J. / Xiao, Y. / Liu, J. / Zhang, W. / Zhang, L. / Jia, G.F. | |||||||||
Funding support | China, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Structural insights into FTO's catalytic mechanism for the demethylation of multiple RNA substrates. Authors: Zhang, X. / Wei, L.H. / Wang, Y. / Xiao, Y. / Liu, J. / Zhang, W. / Yan, N. / Amu, G. / Tang, X. / Zhang, L. / Jia, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zmd.cif.gz | 356.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zmd.ent.gz | 284.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zmd_validation.pdf.gz | 531.6 KB | Display | wwPDB validaton report |
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Full document | 5zmd_full_validation.pdf.gz | 625.1 KB | Display | |
Data in XML | 5zmd_validation.xml.gz | 71.1 KB | Display | |
Data in CIF | 5zmd_validation.cif.gz | 93.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/5zmd ftp://data.pdbj.org/pub/pdb/validation_reports/zm/5zmd | HTTPS FTP |
-Related structure data
Related structure data | 3lfmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53312.223 Da / Num. of mol.: 4 / Mutation: Q86K, Q306K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTO, KIAA1752 / Production host: Escherichia coli (E. coli) 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 #2: DNA chain | Mass: 2719.823 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) DNA launch vector pDE-GFP2 (others) #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-OGA / #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: 3.03 Å3/Da / Density % sol: 64.45 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 180 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9765 Å |
Detector | Type: BRUKER SMART 6500 / Detector: CCD / Date: Apr 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 41219 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.292 / Rsym value: 0.149 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 7.1 % / Rmerge(I) obs: 2.017 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.852 / Rpim(I) all: 0.811 / Rsym value: 1.224 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LFM Resolution: 3.3→35.17 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→35.17 Å
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Refine LS restraints |
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LS refinement shell |
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