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- PDB-1wyw: Crystal Structure of SUMO1-conjugated thymine DNA glycosylase -

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Basic information

Entry
Database: PDB / ID: 1wyw
TitleCrystal Structure of SUMO1-conjugated thymine DNA glycosylase
Components
  • G/T mismatch-specific thymine DNA glycosylase
  • Ubiquitin-like protein SMT3C
KeywordsHYDROLASE
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 / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins ...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 / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / base-excision repair, AP site formation / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of delayed rectifier potassium channel activity / PML body organization / negative regulation of DNA binding / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / depyrimidination / negative regulation of action potential / nuclear stress granule / DNA N-glycosylase activity / sodium ion binding / mismatched DNA binding / SUMO binding / small protein activating enzyme binding / Displacement of DNA glycosylase by APEX1 / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / XY body / regulation of calcium ion transmembrane transport / uracil DNA N-glycosylase activity / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / chloride ion binding / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / transcription factor binding / ubiquitin-specific protease binding / cellular response to cadmium ion / roof of mouth development / SUMOylation of transcription factors / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / regulation of embryonic development / protein sumoylation / potassium channel regulator activity / Regulation of IFNG signaling / postsynaptic cytosol / nuclear pore / transporter activator activity / negative regulation of DNA-binding transcription factor activity / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / Transcriptional and post-translational regulation of MITF-M expression and activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / SUMOylation of transcription cofactors / protein kinase C binding / SUMOylation of chromatin organization proteins / epigenetic regulation of gene expression / transcription coregulator activity / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / base-excision repair / PML body / PKR-mediated signaling / regulation of protein stability / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / double-stranded DNA binding / nuclear membrane / DNA-binding transcription factor binding / damaged DNA binding / nucleic acid binding / protein stabilization / nuclear speck / nuclear body / protein domain specific binding / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding / magnesium ion binding / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
G/T mismatch-specific thymine DNA glycosylasee TDG-like, eukaryotes / Uracil DNA glycosylase family 2 / Small ubiquitin-related modifier 1, Ubl domain / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Uracil-DNA glycosylase-like domain superfamily ...G/T mismatch-specific thymine DNA glycosylasee TDG-like, eukaryotes / Uracil DNA glycosylase family 2 / Small ubiquitin-related modifier 1, Ubl domain / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Uracil-DNA glycosylase-like domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 1 / G/T mismatch-specific thymine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBaba, D. / Maita, N. / Jee, J.G. / Uchimura, Y. / Saitoh, H. / Sugasawa, K. / Hanaoka, F. / Tochio, H. / Hiroaki, H. / Shirakawa, M.
CitationJournal: Nature / Year: 2005
Title: Crystal structure of thymine DNA glycosylase conjugated to SUMO-1.
Authors: Baba, D. / Maita, N. / Jee, J.G. / Uchimura, Y. / Saitoh, H. / Sugasawa, K. / Hanaoka, F. / Tochio, H. / Hiroaki, H. / Shirakawa, M.
History
DepositionFeb 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
B: Ubiquitin-like protein SMT3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,57711
Polymers37,3272
Non-polymers2519
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-76 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.212, 70.420, 106.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 26177.049 Da / Num. of mol.: 1 / Fragment: central region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q13569, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Protein Ubiquitin-like protein SMT3C / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein UBL1 / Ubiquitin-related protein ...Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein UBL1 / Ubiquitin-related protein SUMO-1 / GAP modifying protein 1 / GMP1 / Sentrin / OK/SW-cl.43


Mass: 11149.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT-E1E2S1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63165

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Non-polymers , 4 types, 177 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG3350, 0.1M Tris, 0.2M Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mMHEPES11
2150 mM11NaCl
31 mMdithiothreitol11
420 mg/mlprotein11
525 %PEG335012
60.2 M12MgCl2
70.1 MTris-HCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 19228 / Num. obs: 19228 / % possible obs: 100 % / Redundancy: 19 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.5 / Num. unique all: 53244 / Rsym value: 0.31 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.35

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MUG, 1EUV

1mug

1euv


Resolution: 2.1→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 931 -RANDOM
Rwork0.205 ---
all-19113 --
obs-19113 100 %-
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 9 168 2538
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0053
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d22.41
X-RAY DIFFRACTIONc_improper_angle_d0.838
LS refinement shellResolution: 2.1→2.17 Å
RfactorNum. reflection% reflection
Rfree0.309 78 -
Rwork0.219 --
obs-1846 100 %
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.41
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.838
LS refinement shell
*PLUS
Rfactor Rfree: 0.309 / Rfactor Rwork: 0.219

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