[English] 日本語
Yorodumi
- PDB-5exh: Crystal structure of mTET3-CXXC domain in complex with 5-carboxyl... -

+
Open data


ID or keywords:

Loading...

-
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 / DNA 5-methylcytosine dioxygenase activity / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / positive regulation of gene expression via chromosomal CpG island demethylation / protein O-linked glycosylation / male pronucleus / methyl-CpG binding / female pronucleus / chromosome ...epigenetic programing of male pronucleus / methylcytosine dioxygenase / DNA 5-methylcytosine dioxygenase activity / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / positive regulation of gene expression via chromosomal CpG island demethylation / protein O-linked glycosylation / male pronucleus / methyl-CpG binding / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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