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- PDB-5zmd: Crystal structure of FTO in complex with m6dA modified ssDNA -

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Basic information

Entry
Database: PDB / ID: 5zmd
TitleCrystal structure of FTO in complex with m6dA modified ssDNA
Components
  • Alpha-ketoglutarate-dependent dioxygenase FTO
  • DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3')
KeywordsOXIDOREDUCTASE/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 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
: / N-OXALYLGLYCINE / DNA / Alpha-ketoglutarate-dependent dioxygenase FTO
Similarity search - Component
Biological speciesHomo sapiens (human)
DNA launch vector pDE-GFP2 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZhang, X. / Wei, L.H. / Luo, J. / Xiao, Y. / Liu, J. / Zhang, W. / Zhang, L. / Jia, G.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21432002 China
National Natural Science Foundation of China21722802 China
CitationJournal: 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
DepositionApr 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase FTO
B: DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3')
C: Alpha-ketoglutarate-dependent dioxygenase FTO
D: DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3')
E: Alpha-ketoglutarate-dependent dioxygenase FTO
F: DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3')
G: Alpha-ketoglutarate-dependent dioxygenase FTO
H: DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,93616
Polymers224,1288
Non-polymers8088
Water32418
1
A: Alpha-ketoglutarate-dependent dioxygenase FTO
B: DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3')
C: Alpha-ketoglutarate-dependent dioxygenase FTO
D: DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4688
Polymers112,0644
Non-polymers4044
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Alpha-ketoglutarate-dependent dioxygenase FTO
F: DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3')
G: Alpha-ketoglutarate-dependent dioxygenase FTO
H: DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4688
Polymers112,0644
Non-polymers4044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.736, 160.033, 276.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein
Alpha-ketoglutarate-dependent dioxygenase FTO / Fat mass and obesity-associated 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
DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3')


Mass: 2719.823 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) DNA launch vector pDE-GFP2 (others)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.03 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350, pH 7.0

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Data collection

DiffractionMean temperature: 180 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9765 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Apr 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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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: 3LFM

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
RfactorNum. reflection% reflection
Rfree0.292 2051 5 %
Rwork0.271 --
obs0.272 41003 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→35.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13034 732 44 18 13828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02114203
X-RAY DIFFRACTIONf_angle_d2.09719372
X-RAY DIFFRACTIONf_dihedral_angle_d28.125314
X-RAY DIFFRACTIONf_chiral_restr0.1192097
X-RAY DIFFRACTIONf_plane_restr0.0132351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2978-3.37450.36831220.38212322X-RAY DIFFRACTION91
3.3745-3.45880.38091470.35272565X-RAY DIFFRACTION100
3.4588-3.55220.32661420.34142594X-RAY DIFFRACTION100
3.5522-3.65660.33691360.32012578X-RAY DIFFRACTION100
3.6566-3.77450.34861270.31122577X-RAY DIFFRACTION100
3.7745-3.90930.37211250.30972632X-RAY DIFFRACTION100
3.9093-4.06560.29741460.27242600X-RAY DIFFRACTION100
4.0656-4.25030.29071220.26262586X-RAY DIFFRACTION100
4.2503-4.4740.23491240.25022622X-RAY DIFFRACTION100
4.474-4.75370.251290.24132644X-RAY DIFFRACTION100
4.7537-5.11970.28721300.25122606X-RAY DIFFRACTION100
5.1197-5.6330.26791410.26752637X-RAY DIFFRACTION100
5.633-6.44380.31511610.27242624X-RAY DIFFRACTION100
6.4438-8.10210.26111490.26012667X-RAY DIFFRACTION100
8.1021-35.16820.25331500.2222698X-RAY DIFFRACTION98

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