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- PDB-7wcv: Co-crystal structure of FTO bound to 6e -

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Basic information

Entry
Database: PDB / ID: 7wcv
TitleCo-crystal structure of FTO bound to 6e
ComponentsAlpha-ketoglutarate-dependent dioxygenase FTO
KeywordsOXIDOREDUCTASE / RNA demethylase / 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 / : ...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
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
Chem-943 / 2-OXOGLUTARIC ACID / : / Alpha-ketoglutarate-dependent dioxygenase FTO
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYang, C.-G. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21725801 China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Activity Relationships and Antileukemia Effects of the Tricyclic Benzoic Acid FTO Inhibitors.
Authors: Liu, Z. / Duan, Z. / Zhang, D. / Xiao, P. / Zhang, T. / Xu, H. / Wang, C.H. / Rao, G.W. / Gan, J. / Huang, Y. / Yang, C.G. / Dong, Z.
History
DepositionDec 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)57,0214
Polymers56,4611
Non-polymers5603
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-4 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.759, 141.759, 83.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 / 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: 56460.641 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 ...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-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-943 / 2-[[2,6-bis(chloranyl)-4-pyridin-4-yl-phenyl]amino]benzoic acid


Mass: 359.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H12Cl2N2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium citrate, pH 5.6, 11.5% (w/v) polyethylene glycol (PEG) 3350,8% isopropanol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9735 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 2.3→28.82 Å / Num. obs: 27777 / % possible obs: 99.6 % / Redundancy: 6 % / Biso Wilson estimate: 58.82 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 31.2
Reflection shellResolution: 2.3→28.82 Å / Rmerge(I) obs: 0.65 / Num. unique obs: 27777

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KQN

4kqn


Resolution: 2.3→28.817 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 1394 5.04 %
Rwork0.2025 26291 -
obs0.2043 27685 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.82 Å2 / Biso mean: 76.3443 Å2 / Biso min: 38.03 Å2
Refinement stepCycle: final / Resolution: 2.3→28.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 35 26 3419
Biso mean--81.23 64.96 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043476
X-RAY DIFFRACTIONf_angle_d0.6464740
X-RAY DIFFRACTIONf_chiral_restr0.047524
X-RAY DIFFRACTIONf_plane_restr0.006615
X-RAY DIFFRACTIONf_dihedral_angle_d15.4752055
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.38220.34431260.31072674100
2.3822-2.47760.28591480.28592636100
2.4776-2.59030.29171430.2578259799
2.5903-2.72670.29681480.2526264399
2.7267-2.89740.27231360.2427260999
2.8974-3.12090.27551450.2312620100
3.1209-3.43450.25631570.22432631100
3.4345-3.93040.28621370.2151260098
3.9304-4.94780.19091310.1641262999
4.9478-28.8170.19551230.17222652100
Refinement TLS params.Method: refined / Origin x: -0.4015 Å / Origin y: -24.3921 Å / Origin z: -2.2658 Å
111213212223313233
T0.4083 Å20.0324 Å2-0.0382 Å2-0.413 Å20.0492 Å2--0.3754 Å2
L3.9173 °21.9787 °21.4145 °2-2.6793 °20.88 °2--1.5707 °2
S0.2519 Å °0.1506 Å °-0.4474 Å °0.2596 Å °0.0094 Å °-0.1535 Å °0.338 Å °0.2351 Å °-0.2424 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA28 - 1550
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allE1 - 38
4X-RAY DIFFRACTION1allB1

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