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- PDB-6akw: Crystal structure of RNA dioxygenase bound with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 6akw
TitleCrystal structure of RNA dioxygenase bound with an inhibitor
ComponentsAlpha-ketoglutarate-dependent dioxygenase FTO
KeywordsOXIDOREDUCTASE / RNA demethylase / inhibitor / oxidation / RNA BINDING PROTEIN
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 demethylation ...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 demethylation / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / 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
FTO C-terminal domain / Alpha-ketoglutarate-dependent dioxygenase FTO, C-terminal / Alpha-ketoglutarate-dependent dioxygenase FTO, catalytic domain / Alpha-ketoglutarate-dependent dioxygenase FTO / FTO, C-terminal domain superfamily / FTO catalytic domain / FTO C-terminal domain / FTO catalytic domain / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily ...FTO C-terminal domain / Alpha-ketoglutarate-dependent dioxygenase FTO, C-terminal / Alpha-ketoglutarate-dependent dioxygenase FTO, catalytic domain / Alpha-ketoglutarate-dependent dioxygenase FTO / FTO, C-terminal domain superfamily / FTO catalytic domain / FTO C-terminal domain / FTO catalytic domain / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-8S3 / 2-OXOGLUTARIC ACID / Alpha-ketoglutarate-dependent dioxygenase FTO
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYang, C.-G. / Huang, Y. / Gan, J.
CitationJournal: Cancer Cell / Year: 2019
Title: Small-Molecule Targeting of Oncogenic FTO Demethylase in Acute Myeloid Leukemia.
Authors: Huang, Y. / Su, R. / Sheng, Y. / Dong, L. / Dong, Z. / Xu, H. / Ni, T. / Zhang, Z.S. / Zhang, T. / Li, C. / Han, L. / Zhu, Z. / Lian, F. / Wei, J. / Deng, Q. / Wang, Y. / Wunderlich, M. / ...Authors: Huang, Y. / Su, R. / Sheng, Y. / Dong, L. / Dong, Z. / Xu, H. / Ni, T. / Zhang, Z.S. / Zhang, T. / Li, C. / Han, L. / Zhu, Z. / Lian, F. / Wei, J. / Deng, Q. / Wang, Y. / Wunderlich, M. / Gao, Z. / Pan, G. / Zhong, D. / Zhou, H. / Zhang, N. / Gan, J. / Jiang, H. / Mulloy, J.C. / Qian, Z. / Chen, J. / Yang, C.G.
History
DepositionSep 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase FTO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0493
Polymers56,5261
Non-polymers5232
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint3 kcal/mol
Surface area20310 Å2
Unit cell
Length a, b, c (Å)141.388, 141.388, 83.608
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase FTO / Fat mass and obesity-associated protein


Mass: 56525.668 Da / Num. of mol.: 1
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: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-8S3 / 2-[[2,6-bis(chloranyl)-4-(3,5-dimethyl-1,2-oxazol-4-yl)phenyl]amino]benzoic acid


Mass: 377.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14Cl2N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 100 mM sodium citrate, 12% PEG 3350, 8% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9735 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 31725 / % possible obs: 100 % / Redundancy: 7.1 % / Rsym value: 0.067 / Net I/σ(I): 27.3
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 3187 / Rsym value: 0.804

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QKN

4qkn


Resolution: 2.2→28.745 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 2.04 / Phase error: 28.75
RfactorNum. reflection% reflection
Rfree0.2544 1409 5.04 %
Rwork0.2122 --
obs0.2144 27969 88.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 35 153 3656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023606
X-RAY DIFFRACTIONf_angle_d0.6514900
X-RAY DIFFRACTIONf_dihedral_angle_d15.112152
X-RAY DIFFRACTIONf_chiral_restr0.04528
X-RAY DIFFRACTIONf_plane_restr0.004638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1985-2.27710.2879450.28211146X-RAY DIFFRACTION37
2.2771-2.36820.32521100.27771839X-RAY DIFFRACTION62
2.3682-2.47590.37621220.2712565X-RAY DIFFRACTION84
2.4759-2.60640.28931540.25353007X-RAY DIFFRACTION99
2.6064-2.76960.29681540.24432975X-RAY DIFFRACTION100
2.7696-2.98320.33021590.24243030X-RAY DIFFRACTION100
2.9832-3.2830.26241820.23822974X-RAY DIFFRACTION100
3.283-3.75720.24061430.20543029X-RAY DIFFRACTION100
3.7572-4.73020.22051690.17283002X-RAY DIFFRACTION100
4.7302-28.74770.1991710.17252993X-RAY DIFFRACTION100

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