+Open data
-Basic information
Entry | Database: PDB / ID: 9atn | ||||||
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Title | NMR structure of the MLL4 PHD2/3 fingers in complex with ASXL2 | ||||||
Components |
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Keywords | TRANSFERASE/PROTEIN BINDING / MLL4 / transcription / PROTEIN BINDING / TRANSFERASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information beta-catenin-TCF complex assembly / PR-DUB complex / oocyte growth / positive regulation of peroxisome proliferator activated receptor signaling pathway / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / histone H3K4 methyltransferase activity / peroxisome proliferator activated receptor binding ...beta-catenin-TCF complex assembly / PR-DUB complex / oocyte growth / positive regulation of peroxisome proliferator activated receptor signaling pathway / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / histone H3K4 methyltransferase activity / peroxisome proliferator activated receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / oogenesis / Formation of WDR5-containing histone-modifying complexes / positive regulation of fat cell differentiation / Deactivation of the beta-catenin transactivating complex / animal organ morphogenesis / heterochromatin formation / 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 / UCH proteinases / methylation / transcription coactivator activity / transcription cis-regulatory region binding / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Zhang, Y. / Zandian, M. / Kutateladze, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers. Authors: Zhang, Y. / Xie, G. / Lee, J.E. / Zandian, M. / Sudarshan, D. / Estavoyer, B. / Benz, C. / Viita, T. / Asgaritarghi, G. / Lachance, C. / Messmer, C. / Simonetti, L. / Sinha, V.K. / Lambert, ...Authors: Zhang, Y. / Xie, G. / Lee, J.E. / Zandian, M. / Sudarshan, D. / Estavoyer, B. / Benz, C. / Viita, T. / Asgaritarghi, G. / Lachance, C. / Messmer, C. / Simonetti, L. / Sinha, V.K. / Lambert, J.P. / Chen, Y.W. / Wang, S.P. / Ivarsson, Y. / Affar, E.B. / Cote, J. / Ge, K. / Kutateladze, T.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9atn.cif.gz | 518.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9atn.ent.gz | 433.7 KB | Display | PDB format |
PDBx/mmJSON format | 9atn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9atn_validation.pdf.gz | 550 KB | Display | wwPDB validaton report |
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Full document | 9atn_full_validation.pdf.gz | 991.9 KB | Display | |
Data in XML | 9atn_validation.xml.gz | 64.2 KB | Display | |
Data in CIF | 9atn_validation.cif.gz | 83.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/9atn ftp://data.pdbj.org/pub/pdb/validation_reports/at/9atn | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11014.908 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 (E. coli) References: UniProt: O14686, [histone H3]-lysine4 N-methyltransferase | ||
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#2: Protein/peptide | Mass: 1987.347 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASXL2, ASXH2, KIAA1685 / Production host: Escherichia coli (E. coli) / References: UniProt: Q76L83 | ||
#3: Chemical | ChemComp-ZN / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 1.5 mM 13C, 15N MLL4 PHD2,3, 25 mM TRIS, 150 mM sodium chloride, 3 mM DTT, 93% H2O/7% D2O Label: U-13C, U-15N MLL4 PHD2,3 - C-ASXL2 / Solvent system: 93% H2O/7% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 150 mM / Label: NMR Buffer / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 60 / Conformers submitted total number: 15 |