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- PDB-4fnc: Human TDG in a post-reactive complex with 5-hydroxymethyluracil (5hmU) -

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Basic information

Entry
Database: PDB / ID: 4fnc
TitleHuman TDG in a post-reactive complex with 5-hydroxymethyluracil (5hmU)
Components
  • DNA (28-MER)
  • DNA (29-MER)
  • G/T mismatch-specific thymine DNA glycosylase
KeywordsHYDROLASE/DNA / base excision repair / HYDROLASE-DNA complex
Function / homology
Function and homology information


G/U mismatch-specific uracil-DNA glycosylase activity / thymine-DNA glycosylase / G/T mismatch-specific thymine-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / sodium ion binding / depyrimidination / DNA N-glycosylase activity ...G/U mismatch-specific uracil-DNA glycosylase activity / thymine-DNA glycosylase / G/T mismatch-specific thymine-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / sodium ion binding / depyrimidination / DNA N-glycosylase activity / mismatched DNA binding / SUMO binding / Displacement of DNA glycosylase by APEX1 / uracil DNA N-glycosylase activity / chloride ion binding / regulation of embryonic development / SUMOylation of DNA damage response and repair proteins / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / protein kinase C binding / epigenetic regulation of gene expression / transcription coregulator activity / base-excision repair / PML body / double-stranded DNA binding / DNA-binding transcription factor binding / damaged DNA binding / nucleic acid binding / protein domain specific binding / magnesium ion binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane
Similarity search - Function
G/T mismatch-specific thymine DNA glycosylasee TDG-like, eukaryotes / Uracil DNA glycosylase family 2 / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-HYDROXYMETHYL URACIL / DNA / DNA (> 10) / G/T mismatch-specific thymine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å
AuthorsHashimoto, H. / Hong, S. / Bhagwat, A.S. / Zhang, X. / Cheng, X.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation.
Authors: Hashimoto, H. / Hong, S. / Bhagwat, A.S. / Zhang, X. / Cheng, X.
History
DepositionJun 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Jul 9, 2014Group: Non-polymer description
Revision 1.4Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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_validate_polymer_linkage / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G/T mismatch-specific thymine DNA glycosylase
C: DNA (28-MER)
D: DNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6374
Polymers40,4953
Non-polymers1421
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-23 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.96, 53.72, 81.56
Angle α, β, γ (deg.)90.00, 96.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein G/T mismatch-specific thymine DNA glycosylase / Thymine-DNA glycosylase


Mass: 23070.670 Da / Num. of mol.: 1
Fragment: human TDG glycosylase domain, UNP residues 111-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDG / Plasmid: pXC1056 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13569, thymine-DNA glycosylase
#2: DNA chain DNA (28-MER)


Mass: 8646.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide synthesis
#3: DNA chain DNA (29-MER)


Mass: 8777.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide synthesis
#4: Chemical ChemComp-HMU / 5-HYDROXYMETHYL URACIL / 5-(HYDROXYMETHYL)PYRIMIDINE-2,4(1H,3H)-DIONE


Mass: 142.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% polyethylene glycol (PEG) 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2011
Details: Rosenbaum-Rock monochromator high-resolution double-crystal Si(220) sagittal focusing, Rosenbaum-Rock vertical focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→39.161 Å / Num. obs: 13702 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 58.71 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 25.3
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1282 / % possible all: 93.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RBA

2rba


Resolution: 2.493→39.161 Å / SU ML: 0.86 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 680 4.97 %random
Rwork0.2239 ---
obs0.2259 13673 98.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.807 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-25.2992 Å2-0 Å216.1207 Å2
2---10.7805 Å20 Å2
3----14.5187 Å2
Refinement stepCycle: LAST / Resolution: 2.493→39.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 1139 10 38 2712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032851
X-RAY DIFFRACTIONf_angle_d0.8634097
X-RAY DIFFRACTIONf_dihedral_angle_d23.6141126
X-RAY DIFFRACTIONf_chiral_restr0.056453
X-RAY DIFFRACTIONf_plane_restr0.003329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.493-2.68540.49231190.3842476X-RAY DIFFRACTION95
2.6854-2.95560.3921530.33142583X-RAY DIFFRACTION100
2.9556-3.38310.31721430.23072596X-RAY DIFFRACTION100
3.3831-4.26150.23671230.21692644X-RAY DIFFRACTION100
4.2615-39.16560.21581420.18532694X-RAY DIFFRACTION100

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