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- PDB-5exh: Crystal structure of mTET3-CXXC domain in complex with 5-carboxyl... -

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Basic information

Entry
Database: PDB / ID: 5exh
TitleCrystal structure of mTET3-CXXC domain in complex with 5-carboxylcytosine DNA at 1.3 Angstroms resolution.
Components
  • DNA (5'-D(*GP*AP*AP*TP*CP*(1CC)P*GP*GP*AP*TP*TP*C)-3')
  • Methylcytosine dioxygenase TET3
KeywordsOXIDOREDUCTASE/DNA / mouse Tet3 / complex / 5-carboxylcytosine / reader / OXIDOREDUCTASE-DNA complex
Function / homology
Function and homology information


epigenetic programing of male pronucleus / methylcytosine dioxygenase / 5-methylcytosine dioxygenase activity / : / chromosomal 5-methylcytosine DNA demethylation pathway / protein O-linked glycosylation / methyl-CpG binding / male pronucleus / female pronucleus / chromosome ...epigenetic programing of male pronucleus / methylcytosine dioxygenase / 5-methylcytosine dioxygenase activity / : / chromosomal 5-methylcytosine DNA demethylation pathway / protein O-linked glycosylation / methyl-CpG binding / male pronucleus / female pronucleus / chromosome / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Methylcytosine dioxygenase TET1/2/3 / : / Oxygenase domain of the 2OGFeDO superfamily / 2OGFeDO, oxygenase domain / Oxygenase domain of the 2OGFeDO superfamily / Zinc finger, CXXC-type / Zinc finger CXXC-type profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / Methylcytosine dioxygenase TET3 / Methylcytosine dioxygenase TET3
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSong, J.
CitationJournal: Cell Rep / Year: 2016
Title: Tet3 Reads 5-Carboxylcytosine through Its CXXC Domain and Is a Potential Guardian against Neurodegeneration.
Authors: Jin, S.G. / Zhang, Z.M. / Dunwell, T.L. / Harter, M.R. / Wu, X. / Johnson, J. / Li, Z. / Liu, J. / Szabo, P.E. / Lu, Q. / Xu, G.L. / Song, J. / Pfeifer, G.P.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*AP*AP*TP*CP*(1CC)P*GP*GP*AP*TP*TP*C)-3')
B: DNA (5'-D(*GP*AP*AP*TP*CP*(1CC)P*GP*GP*AP*TP*TP*C)-3')
C: Methylcytosine dioxygenase TET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0455
Polymers12,9143
Non-polymers1312
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-19 kcal/mol
Surface area7060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.959, 27.230, 47.060
Angle α, β, γ (deg.)90.00, 104.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*GP*AP*AP*TP*CP*(1CC)P*GP*GP*AP*TP*TP*C)-3')


Mass: 3706.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide Methylcytosine dioxygenase TET3 / TET3 isoform 1 / Tet methylcytosine deoxygenase 3 isoform


Mass: 5501.648 Da / Num. of mol.: 1 / Fragment: CXXC domain (UNP residues 51-96)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tet3 / Production host: Escherichia coli (E. coli)
References: UniProt: L0HN04, UniProt: Q8BG87*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation ...References: UniProt: L0HN04, UniProt: Q8BG87*PLUS, 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 1.8 Å3/Da / Density % sol: 31.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, pH 7.5, 50 mM, calcium chloride, 41% PEG200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 23079 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 25
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 5.14 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data scaling
Cootmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HP1

4hp1


Resolution: 1.3→32.633 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 1180 5.12 %
Rwork0.168 --
obs0.169 23064 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→32.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms353 491 2 230 1076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007920
X-RAY DIFFRACTIONf_angle_d1.5231332
X-RAY DIFFRACTIONf_dihedral_angle_d28.325396
X-RAY DIFFRACTIONf_chiral_restr0.071147
X-RAY DIFFRACTIONf_plane_restr0.00687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2956-1.35460.18991280.20472695X-RAY DIFFRACTION98
1.3546-1.4260.22421360.19182751X-RAY DIFFRACTION100
1.426-1.51540.18331460.17642695X-RAY DIFFRACTION100
1.5154-1.63230.19451480.16192728X-RAY DIFFRACTION100
1.6323-1.79660.17781430.1542751X-RAY DIFFRACTION100
1.7966-2.05650.17811700.16182714X-RAY DIFFRACTION100
2.0565-2.59090.19651550.17172761X-RAY DIFFRACTION100
2.5909-32.64350.1841540.16572789X-RAY DIFFRACTION98

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