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- PDB-7ckk: Structural complex of FTO bound with Dac51 -

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Basic information

Entry
Database: PDB / ID: 7ckk
TitleStructural complex of FTO bound with Dac51
ComponentsAlpha-ketoglutarate-dependent dioxygenase FTO
KeywordsRNA BINDING PROTEIN / Inhibitor / Complex / Demethylase
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-B6C / N-OXALYLGLYCINE / Alpha-ketoglutarate-dependent dioxygenase FTO
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsYang, C. / Gan, J.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
CitationJournal: Cell Metab. / Year: 2021
Title: Tumors exploit FTO-mediated regulation of glycolytic metabolism to evade immune surveillance.
Authors: Liu, Y. / Liang, G. / Xu, H. / Dong, W. / Dong, Z. / Qiu, Z. / Zhang, Z. / Li, F. / Huang, Y. / Li, Y. / Wu, J. / Yin, S. / Zhang, Y. / Guo, P. / Liu, J. / Xi, J.J. / Jiang, P. / Han, D. / Yang, C.G. / Xu, M.M.
History
DepositionJul 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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)54,9173
Polymers54,3781
Non-polymers5382
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint1 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.124, 142.124, 84.539
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: 54378.297 Da / Num. of mol.: 1 / Mutation: K45L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTO, KIAA1752
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#3: Chemical ChemComp-B6C / 2-{[2,6-dichloro-4-(3,5-dimethyl-1H-pyrazol-4-yl)phenyl]amino}-N-hydroxybenzamide


Mass: 391.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16Cl2N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.02 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate (pH 5.8), 12 % (w/v) polyethylene glycol 3350, 8 % isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9735 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 26488 / % possible obs: 99.7 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Χ2: 0.976 / Net I/σ(I): 13.9 / Num. measured all: 260158
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.438.81.16226340.7520.4031.2320.86699.2
2.43-2.539.70.86326280.8670.2890.9110.875100
2.53-2.65100.62326870.9470.2050.6560.922100
2.65-2.79100.44626440.0360.1750.4851.0399.8
2.79-2.969.50.21526470.9880.0730.2270.94299.5
2.96-3.1910.60.12926500.9950.0410.1361.016100
3.19-3.5110.40.07826690.9970.0250.0821.101100
3.51-4.029.80.05326450.9970.0180.0561.18299.9
4.02-5.069.40.03926270.9970.0140.0421.13498.8
5.06-30100.02826570.9990.010.030.6899.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QKN

4qkn


Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.889 / SU B: 7.242 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 1250 5.2 %RANDOM
Rwork0.2207 ---
obs0.2228 22821 90.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.13 Å2 / Biso mean: 37.38 Å2 / Biso min: 11.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 36 71 3468
Biso mean--48.5 28.26 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193480
X-RAY DIFFRACTIONr_bond_other_d0.0010.023193
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9534733
X-RAY DIFFRACTIONr_angle_other_deg0.91237299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3524.036166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66615555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4961522
X-RAY DIFFRACTIONr_chiral_restr0.0730.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213949
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02827
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 42 -
Rwork0.26 1056 -
all-1098 -
obs--56.48 %

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