[English] 日本語
Yorodumi
- PDB-8u2y: Solution structure of the PHD6 finger of MLL4 bound to TET3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u2y
TitleSolution structure of the PHD6 finger of MLL4 bound to TET3
Components
  • Histone-lysine N-methyltransferase 2D
  • Methylcytosine dioxygenase TET3
KeywordsGENE REGULATION / KMT2D / TET3 / chromatin / epigenetics
Function / homology
Function and homology information


epigenetic programing of male pronucleus / : / beta-catenin-TCF complex assembly / : / 5-methylcytosine catabolic process / 5-methylcytosine dioxygenase activity / oocyte growth / TET1,2,3 and TDG demethylate DNA / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity ...epigenetic programing of male pronucleus / : / beta-catenin-TCF complex assembly / : / 5-methylcytosine catabolic process / 5-methylcytosine dioxygenase activity / oocyte growth / TET1,2,3 and TDG demethylate DNA / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / : / histone H3K4 trimethyltransferase activity / oxidative demethylation / protein O-linked glycosylation / MLL3/4 complex / methyl-CpG binding / male pronucleus / female pronucleus / histone H3K4 methyltransferase activity / positive regulation of intracellular estrogen receptor signaling pathway / oogenesis / Formation of WDR5-containing histone-modifying complexes / heterochromatin formation / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / response to estrogen / chromosome / histone binding / methylation / transcription coactivator activity / transcription cis-regulatory region binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase 2D / KMT2D, ePHD1 domain / KMT2D, ePHD2 domain / : / : / Methylcytosine dioxygenase TET1/2/3 / Oxygenase domain of the 2OGFeDO superfamily / 2OGFeDO, oxygenase domain / Oxygenase domain of the 2OGFeDO superfamily / FY-rich, N-terminal ...Histone-lysine N-methyltransferase 2D / KMT2D, ePHD1 domain / KMT2D, ePHD2 domain / : / : / Methylcytosine dioxygenase TET1/2/3 / Oxygenase domain of the 2OGFeDO superfamily / 2OGFeDO, oxygenase domain / Oxygenase domain of the 2OGFeDO superfamily / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / PHD-zinc-finger like domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain profile. / SET domain / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone-lysine N-methyltransferase 2D / Methylcytosine dioxygenase TET3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMohid, S.A. / Zandian, M. / Zhang, Y. / Kutateladze, T.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Structure / Year: 2024
Title: MLL4 binds TET3.
Authors: Becht, D.C. / Mohid, S.A. / Lee, J.E. / Zandian, M. / Benz, C. / Biswas, S. / Sinha, V.K. / Ivarsson, Y. / Ge, K. / Zhang, Y. / Kutateladze, T.G.
History
DepositionSep 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methylcytosine dioxygenase TET3
B: Histone-lysine N-methyltransferase 2D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8224
Polymers7,6922
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Methylcytosine dioxygenase TET3


Mass: 864.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TET3, KIAA0401
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O43151, methylcytosine dioxygenase
#2: Protein Histone-lysine N-methyltransferase 2D / Lysine N-methyltransferase 2D / ALL1-related protein / Myeloid/lymphoid or mixed-lineage leukemia protein 2


Mass: 6826.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2D, ALR, MLL2, MLL4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O14686, [histone H3]-lysine4 N-methyltransferase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D HN(CA)CB
121isotropic23D CBCA(CO)NH
131isotropic23D CC(CO)NH
141isotropic23D HBHA(CO)NH
151isotropic23D HNCA
161isotropic23D H(CCO)NH
171isotropic23D 1H-13C NOESY
181isotropic23D 1H-15N NOESY
191isotropic23D (H)CCH-TOCSY
1101isotropic22D 1H-13C HSQC
1111isotropic22D 1H-15N HSQC
1121isotropic23D 1H-13C NOESY aromatic
1131isotropic21D 1H

-
Sample preparation

DetailsType: solution / Contents: 2.0 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O / Label: 15N-13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 2.0 mM / Component: Protein / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 150 mM / Label: Condition-1 / pH: 7.0 Not defined / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA9002

-
Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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://pdbjlvh1.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