[English] 日本語
Yorodumi
- PDB-4xeg: Structure of the enzyme-product complex resulting from TDG action... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xeg
TitleStructure of the enzyme-product complex resulting from TDG action on a G/hmU mismatch
Components
  • (DNA (28-MER)) x 2
  • G/T mismatch-specific thymine DNA glycosylase
KeywordsHYDROLASE/DNA / DNA glycosylase / abasic site / enzyme-product complex / 5-hydroxymethyluracil / 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
ACETIC ACID / DNA / DNA (> 10) / G/T mismatch-specific thymine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsPozharski, E. / Malik, S.S. / Drohat, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM072711 United States
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA.
Authors: Malik, S.S. / Coey, C.T. / Varney, K.M. / Pozharski, E. / Drohat, A.C.
History
DepositionDec 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,4958
Polymers40,1913
Non-polymers3045
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-21 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.199, 53.393, 82.220
Angle α, β, γ (deg.)90.000, 95.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-554-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 23070.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDG / Production host: Escherichia coli (E. coli) / References: UniProt: Q13569, thymine-DNA glycosylase

-
DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (28-MER)


Mass: 8646.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: DNA chain DNA (28-MER)


Mass: 8473.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

-
Non-polymers , 3 types, 305 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% (w/v) PEG 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.72→39.14 Å / Num. obs: 40036 / % possible obs: 97.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.016 / Net I/σ(I): 23.8 / Num. measured all: 266180
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.72-1.753.80.9181.4502713320.7610.49162.1
9.09-39.146.60.016101194329510.00797.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDS0.1.26data reduction
PHASERphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FNC

4fnc


Resolution: 1.72→39.14 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.258 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 2016 5 %RANDOM
Rwork0.1882 38012 --
obs0.1904 38012 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.21 Å2 / Biso mean: 38.544 Å2 / Biso min: 17.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.03 Å2
2--0.02 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.72→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 1135 20 304 3013
Biso mean--50.92 47.36 -
Num. residues----252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0162967
X-RAY DIFFRACTIONr_bond_other_d0.0020.022236
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.5964255
X-RAY DIFFRACTIONr_angle_other_deg1.19635207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8475205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95224.24773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2915291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.905157
X-RAY DIFFRACTIONr_chiral_restr0.1150.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212544
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02669
X-RAY DIFFRACTIONr_mcbond_it3.4283.27805
X-RAY DIFFRACTIONr_mcbond_other3.4113.258801
X-RAY DIFFRACTIONr_mcangle_it4.2584.8831004
LS refinement shellResolution: 1.718→1.763 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 107 -
Rwork0.393 2041 -
all-2148 -
obs--71.29 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more