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- PDB-9ohs: Crystal structure of human FTO in complex with Ga(III) and ascorbate -

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Basic information

Entry
Database: PDB / ID: 9ohs
TitleCrystal structure of human FTO in complex with Ga(III) and ascorbate
ComponentsAlpha-ketoglutarate-dependent dioxygenase FTO
KeywordsOXIDOREDUCTASE / Fe(II)/2-oxoglutarate-dependent dioxygenase / RNA demethylase / RNA modifying enzyme / AlkB homolog
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 / broad specificity oxidative DNA demethylase activity / oxidative RNA 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 / broad specificity oxidative DNA demethylase activity / oxidative RNA 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 / cytosol / cytoplasm
Similarity search - Function
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 superfamily
Similarity search - Domain/homology
ASCORBIC ACID / GALLIUM (III) ION / Alpha-ketoglutarate-dependent dioxygenase FTO
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.072 Å
AuthorsCalzini, L.O. / Mugridge, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM143000 United States
CitationJournal: Biorxiv / Year: 2025
Title: Differential control of RNA demethylase activity and selectivity by cofactor ascorbate.
Authors: Calzini, L.O. / Warminski, M. / Kowalska, J. / Jemielity, J. / Mugridge, J.S.
History
DepositionMay 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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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)55,1453
Polymers54,8991
Non-polymers2462
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.872, 143.872, 85.241
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase FTO / Fat mass and obesity-associated protein / U6 small nuclear RNA (2'-O-methyladenosine-N(6)-)- ...Fat mass and obesity-associated protein / U6 small nuclear RNA (2'-O-methyladenosine-N(6)-)-demethylase FTO / U6 small nuclear RNA N(6)-methyladenosine-demethylase FTO / mRNA (2'-O-methyladenosine-N(6)-)-demethylase FTO / m6A(m)-demethylase FTO / mRNA N(6)-methyladenosine demethylase FTO / tRNA N1-methyl adenine demethylase FTO


Mass: 54898.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 166-189 were deleted and replaced with a 4xGS linker (GSGSGSGS)
Source: (gene. exp.) Homo sapiens (human) / Gene: FTO, KIAA1752 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta
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 ...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, mRNA N6-methyladenine demethylase
#2: Chemical ChemComp-GA / GALLIUM (III) ION


Mass: 69.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ga
#3: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 3.09 Å3/Da / Density % sol: 60.18 % / Description: Rhombohedral
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 6.5, 1.6M Ammonium sulfate, 10% (v/v) 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.07→100 Å / Num. obs: 12280 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 111.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1285 / Rpim(I) all: 0.04151 / Rrim(I) all: 0.1351 / Net I/σ(I): 14.73
Reflection shellResolution: 3.072→3.182 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.629 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 1234 / CC1/2: 0.283 / Rpim(I) all: 0.5132 / Rrim(I) all: 1.708 / % possible all: 99.84

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSVERSION Jan 19, 2025 BUILT=20250409data reduction
PHASER2.8.3phasing
Coot0.8.9.1model building
XDSVERSION Jan 19, 2025 BUILT=20250409data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.072→41.22 Å / SU ML: 0.4929 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.7325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2529 1225 9.98 %
Rwork0.1929 11049 -
obs0.1992 12274 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.4 Å2
Refinement stepCycle: LAST / Resolution: 3.072→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 0 13 0 3488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01093571
X-RAY DIFFRACTIONf_angle_d1.24554842
X-RAY DIFFRACTIONf_chiral_restr0.059523
X-RAY DIFFRACTIONf_plane_restr0.0082627
X-RAY DIFFRACTIONf_dihedral_angle_d23.24091331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.072-3.190.38271330.3361235X-RAY DIFFRACTION99.85
3.2-3.340.37891370.31541230X-RAY DIFFRACTION100
3.34-3.520.34231230.27241244X-RAY DIFFRACTION99.78
3.52-3.740.29521440.23931204X-RAY DIFFRACTION100
3.74-4.030.27611410.21261242X-RAY DIFFRACTION99.93
4.03-4.430.2291400.18541209X-RAY DIFFRACTION100
4.43-5.070.21441340.16491231X-RAY DIFFRACTION100
5.07-6.380.29821240.19381242X-RAY DIFFRACTION100
6.39-41.220.2071490.15231212X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 21.8105939061 Å / Origin y: -12.4100364545 Å / Origin z: -37.2199558882 Å
111213212223313233
T0.80543396952 Å20.0623035761386 Å20.0638117900453 Å2-0.706985583146 Å2-0.0546070657984 Å2--0.755598527472 Å2
L5.50793436788 °21.81953565627 °21.70508833025 °2-2.97655174701 °21.12216355196 °2--2.40366705575 °2
S0.260730635004 Å °0.531491728085 Å °-0.434753350116 Å °0.331207658369 Å °0.0872018210531 Å °-0.32964915372 Å °0.588992185997 Å °0.268891789122 Å °-0.360652740809 Å °
Refinement TLS groupSelection details: all

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