[English] 日本語
Yorodumi
- PDB-5hf7: TDG enzyme-substrate complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hf7
TitleTDG enzyme-substrate complex
Components
  • (DNA (28-MER)) x 2
  • G/T mismatch-specific thymine DNA glycosylase
KeywordsHYDROLASE/DNA / protein-DNA complex / HYDROLASE-DNA complex
Function / homology
Function and homology information


thymine-DNA glycosylase / G/T mismatch-specific thymine-DNA glycosylase activity / G/U mismatch-specific uracil-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / sodium ion binding / DNA N-glycosylase activity / mismatched DNA binding ...thymine-DNA glycosylase / G/T mismatch-specific thymine-DNA glycosylase activity / G/U mismatch-specific uracil-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / sodium ion binding / 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 / epigenetic regulation of gene expression / protein kinase C binding / transcription coregulator activity / base-excision repair / PML body / double-stranded DNA binding / DNA-binding transcription factor binding / nucleic acid binding / damaged DNA binding / protein domain specific binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / 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
DNA / DNA (> 10) / G/T mismatch-specific thymine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.54 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: 2016
Title: Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues.
Authors: Coey, C.T. / Malik, S.S. / Pidugu, L.S. / Varney, K.M. / Pozharski, E. / Drohat, A.C.
History
DepositionJan 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)


Theoretical massNumber of molelcules
Total (without water)43,0913
Polymers43,0913
Non-polymers00
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-26 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.030, 52.750, 81.340
Angle α, β, γ (deg.)90.00, 95.18, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 25859.010 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
#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: 8585.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M Ammonium chloride, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→32.51 Å / Biso Wilson estimate: 25.82 Å2
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 0.5 / % possible all: 94.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
Aimless0.5.9data scaling
RefinementResolution: 1.54→32.51 Å / Cor.coef. Fo:Fc: 0.9629 / Cor.coef. Fo:Fc free: 0.9548 / SU R Cruickshank DPI: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.08 / SU Rfree Blow DPI: 0.081 / SU Rfree Cruickshank DPI: 0.075
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 2942 4.96 %RANDOM
Rwork0.1858 ---
obs0.1872 59281 97.62 %-
Displacement parametersBiso mean: 44.43 Å2
Baniso -1Baniso -2Baniso -3
1--7.1849 Å20 Å21.2458 Å2
2--1.9443 Å20 Å2
3---5.2406 Å2
Refine analyzeLuzzati coordinate error obs: 0.522 Å
Refinement stepCycle: LAST / Resolution: 1.54→32.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 1143 0 328 3074
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012932HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.984213HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d860SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes314HARMONIC5
X-RAY DIFFRACTIONt_it2932HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion20.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion379SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3292SEMIHARMONIC4
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2729 169 4.76 %
Rwork0.2765 3378 -
all0.2763 3547 -
obs--97.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.44480.59523.2242.72191.43886.51670.2418-0.0608-0.3579-0.0876-0.18170.30120.1586-0.682-0.060.3129-0.0281-0.03730.0565-0.00420.074715.4970.507449.5293
21.45760.25520.23143.06850.42231.59620.03260.0986-0.1129-0.1031-0.0725-0.39780.1220.10180.03990.1671-0.0025-0.0419-0.03610.0163-0.001228.9047.333553.0679
32.18693.4321-0.4476.47250.97529.8224-0.31540.1854-0.218-0.55310.187-0.6516-0.04420.49670.12840.3512-0.02270.0360.06970.03580.102534.580215.906344.2687
45.4179-2.29692.71241.02640.15024.50190.09870.2155-0.1326-0.2169-0.0423-0.24230.07560.2216-0.05640.35680.03080.04670.07390.00790.155435.78355.367446.112
55.8690.0590.8663.00680.46071.43470.0522-0.0911-0.12490.1985-0.1068-0.18680.077-0.13540.05460.2076-0.0109-0.0301-0.01660.0106-0.053325.09488.056357.8445
67.2216-0.77322.32462.134-0.34230.87720.0957-0.2833-0.20510.3737-0.21180.1622-0.0045-0.35140.11610.4362-0.043-0.00380.1850.0041-0.033820.07727.658469.4057
71.81680.72410.14333.96870.42251.87050.044-0.2043-0.03570.7813-0.188-0.4537-0.13780.05840.1440.3381-0.03-0.1770.03550.04650.05333.329515.640966.9936
84.34310.68351.36421.82520.11611.5497-0.17090.13160.2932-0.0565-0.0682-0.2167-0.38720.10870.23920.2322-0.0406-0.0973-0.03170.0448-0.003128.789523.175251.8226
97.1016-0.39522.77094.87261.33824.9384-0.0501-0.1064-0.03470.18780.1146-0.2757-0.17940.2694-0.06450.173-0.0172-0.02650.17480.12310.314746.976819.431256.6108
106.3595-4.8282-2.10684.8687-1.22845.52570.1123-0.3363-0.14090.38080.4545-0.81970.52560.4563-0.56670.79570.1573-0.02540.7384-0.25830.307312.128527.181475.7652
117.83571.0396-3.45474.5048-1.089212.6102-0.06190.21580.45150.1255-0.02010.309-0.4305-0.61430.0820.2989-0.0002-0.15410.1090.0080.124213.172923.352249.2191
121.4216-0.76470.62882.89940.73499.9440.09460.02260.0117-0.444-0.01860.2458-0.3266-0.0514-0.0760.4732-0.0174-0.20240.0622-0.00250.12425.884310.08120.4526
1313.6942-4.19783.59587.0538-4.48116.94280.17820.09030.45660.05520.12130.7799-0.5344-0.4008-0.29950.56670.1231-0.30110.3021-0.04590.2121-3.1168.60547.1411
144.0387-2.85360.433813.32241.21376.55090.1513-0.16530.0176-0.0481-0.0226-0.0515-0.2753-0.2422-0.12870.46850.0135-0.1892-0.0372-0.02310.02677.20736.642319.3034
153.10410.30241.56234.8889-4.25539.4320.1299-0.55780.1802-0.07160.40110.1168-0.7554-0.7014-0.5310.3748-0.0479-0.07390.1945-0.0470.15778.51617.100735.7455
168.7119-2.165-5.54940.98254.83010.326-0.0272-0.59120.54020.8156-0.05980.37-0.9505-0.6860.0870.37720.13960.02160.2175-0.04310.036715.051122.898560.2246
1711.84790.66711.16739.5565-0.09117.44040.516-0.2125-1.5549-0.05390.48390.37960.8031-0.5886-0.99990.80020.0817-0.02710.5571-0.22510.16468.523526.310581.3511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|107 - A|126 }
2X-RAY DIFFRACTION2{ A|127 - A|158 }
3X-RAY DIFFRACTION3{ A|159 - A|173 }
4X-RAY DIFFRACTION4{ A|174 - A|184 }
5X-RAY DIFFRACTION5{ A|185 - A|201 }
6X-RAY DIFFRACTION6{ A|202 - A|213 }
7X-RAY DIFFRACTION7{ A|214 - A|269 }
8X-RAY DIFFRACTION8{ A|270 - A|295 }
9X-RAY DIFFRACTION9{ A|296 - A|301 }
10X-RAY DIFFRACTION10{ C|1 - C|8 }
11X-RAY DIFFRACTION11{ C|9 - C|15 }
12X-RAY DIFFRACTION12{ C|16 - C|28 }
13X-RAY DIFFRACTION13{ D|1 - D|4 }
14X-RAY DIFFRACTION14{ D|5 - D|8 }
15X-RAY DIFFRACTION15{ D|9 - D|15 }
16X-RAY DIFFRACTION16{ D|16 - D|23 }
17X-RAY DIFFRACTION17{ D|24 - D|28 }

+
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