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- PDB-8u2y: Solution structure of the PHD6 finger of MLL4 bound to TET3 -

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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 / methylcytosine dioxygenase / DNA 5-methylcytosine dioxygenase activity / oocyte growth / TET1,2,3 and TDG demethylate DNA / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity ...epigenetic programing of male pronucleus / beta-catenin-TCF complex assembly / methylcytosine dioxygenase / DNA 5-methylcytosine dioxygenase activity / oocyte growth / TET1,2,3 and TDG demethylate DNA / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / positive regulation of gene expression via chromosomal CpG island demethylation / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / protein O-linked glycosylation / MLL3/4 complex / male pronucleus / methyl-CpG binding / female pronucleus / histone H3K4 methyltransferase activity / oogenesis / positive regulation of intracellular estrogen receptor signaling pathway / Formation of WDR5-containing histone-modifying complexes / Chromatin modifications during the maternal to zygotic transition (MZT) / 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 / response to estrogen / Activation of anterior HOX genes in hindbrain development during early embryogenesis / heterochromatin formation / chromosome / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / methylation / transcription coactivator activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA 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 / 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 ...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 / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / PHD-finger / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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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

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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

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NMR measurement

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

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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

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