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- PDB-6o7g: Solution structure of MLL4 PHD6 domain in complex with histone H4... -

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Basic information

Entry
Database: PDB / ID: 6o7g
TitleSolution structure of MLL4 PHD6 domain in complex with histone H4K16ac peptide
Components
  • Histone H4
  • Histone-lysine N-methyltransferase 2D
KeywordsTRANSCRIPTION / MLL4 / PHD finger / H4K16ac / MOF / acetylation / histone / chromatin
Function / homology
Function and homology information


beta-catenin-TCF complex assembly / oocyte growth / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / histone H3K4 methyltransferase activity / oogenesis / positive regulation of intracellular estrogen receptor signaling pathway ...beta-catenin-TCF complex assembly / oocyte growth / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / histone H3K4 methyltransferase activity / oogenesis / positive regulation of intracellular estrogen receptor signaling pathway / Formation of WDR5-containing histone-modifying complexes / 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 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / 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
Similarity search - Function
Histone-lysine N-methyltransferase 2D / KMT2D, ePHD1 domain / KMT2D, ePHD2 domain / : / : / 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 ...Histone-lysine N-methyltransferase 2D / KMT2D, ePHD1 domain / KMT2D, ePHD2 domain / : / : / 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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, Y. / Kutateladze, T.G.
CitationJournal: Nat Commun / Year: 2019
Title: Selective binding of the PHD6 finger of MLL4 to histone H4K16ac links MLL4 and MOF.
Authors: Zhang, Y. / Jang, Y. / Lee, J.E. / Ahn, J. / Xu, L. / Holden, M.R. / Cornett, E.M. / Krajewski, K. / Klein, B.J. / Wang, S.P. / Dou, Y. / Roeder, R.G. / Strahl, B.D. / Rothbart, S.B. / Shi, ...Authors: Zhang, Y. / Jang, Y. / Lee, J.E. / Ahn, J. / Xu, L. / Holden, M.R. / Cornett, E.M. / Krajewski, K. / Klein, B.J. / Wang, S.P. / Dou, Y. / Roeder, R.G. / Strahl, B.D. / Rothbart, S.B. / Shi, X. / Ge, K. / Kutateladze, T.G.
History
DepositionMar 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.1Nov 13, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Histone-lysine N-methyltransferase 2D
A: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6354
Polymers8,5052
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR, fluorescence microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1220 Å2
ΔGint-4 kcal/mol
Surface area4540 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone-lysine N-methyltransferase 2D / Lysine N-methyltransferase 2D / ALL1-related protein / Myeloid/lymphoid or mixed-lineage leukemia protein 2


Mass: 7240.149 Da / Num. of mol.: 1 / Fragment: residues 1503-1562
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-lysine N-methyltransferase
#2: Protein/peptide Histone H4


Mass: 1264.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D CBCA(CO)NH
131isotropic13D C(CO)NH
141isotropic13D HBHA(CO)NH
151isotropic13D HNCA
161isotropic13D H(CCO)NH
191isotropic23D NOESY-HSQC
181isotropic23D filtered NOESY
171isotropic22D filtered TOCSY

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Sample preparation

DetailsType: solution
Contents: 2.5 mM [U-13C; U-15N] MLL4 PHD6, 7.5 mM histone H4K16ac (11-21) peptide, 93% H2O/7% D2O
Details: 2.5 mM 13C/15N-labeled MLL4-PHD6 sample supplemented with 7.5 mM H4K16ac (11-21) peptide
Label: complex / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMMLL4 PHD6[U-13C; U-15N]1
7.5 mMhistone H4K16ac (11-21) peptidenatural abundance1
Sample conditionsDetails: 20 mM Tris-HCl (pH 7.0), 100 mM NaCl, 5 mM DTT and 8% D2O
Ionic strength: 100 mM / Label: conditions_1 / pH: 7 / 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
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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