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- PDB-2ysm: Solution structure of the second and third PHD domain from Histon... -

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Basic information

Entry
Database: PDB / ID: 2ysm
TitleSolution structure of the second and third PHD domain from Histone-lysine N-methyltransferase 2C (KMT2C/MLL3)
ComponentsMyeloid/lymphoid or mixed-lineage leukemia protein 3 homolog
KeywordsTRANSFERASE / PHD domain / Myeloid/lymphoid or mixed-lineage leukemia protein / Histone-lysine N-methyltransferase / H3 lysine-4 specific MLL3 / Homologous to ALR protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


[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 / acyltransferase activity / histone methyltransferase complex / histone methyltransferase activity / Formation of WDR5-containing histone-modifying complexes ...[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 / acyltransferase activity / histone methyltransferase complex / histone methyltransferase activity / Formation of WDR5-containing histone-modifying complexes / response to electrical stimulus / 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 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / methylation / transcription coactivator activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Histone-lysine N-methyltransferase 2C / KMT2C, ePHD1 / KMT2C, ePHD2 / : / : / : / DHHC domain profile. / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / FY-rich, N-terminal ...Histone-lysine N-methyltransferase 2C / KMT2C, ePHD1 / KMT2C, ePHD2 / : / : / : / DHHC domain profile. / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / 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 / Zinc/RING finger domain, C3HC4 (zinc finger) / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Herpes Virus-1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase 2C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQin, X.R. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the first and second PHD domain from Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog
Authors: Qin, X.R. / Hayashi, F. / Yokoyama, S.
History
DepositionApr 3, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2018Group: Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct
Item: _entity_src_gen.pdbx_description / _entity_src_gen.pdbx_host_org_scientific_name / _struct.title
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1415
Polymers11,8801
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8250 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog / Histone-lysine N-methyltransferase / H3 lysine-4 specific MLL3 / Homologous to ALR protein


Mass: 11879.634 Da / Num. of mol.: 1 / Fragment: PHD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLL3, HALR, KIAA1506 / Plasmid: P070115-52 / Production host: cell-free protein synthesis (unknown)
References: UniProt: Q8NEZ4, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: spectrometer_id 1 for 3D_15N_separaed_NOESY; spectrometer_id 2 for 3D_13C_separaed_NOESY;

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Sample preparation

DetailsContents: 0.94mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.05mM ZnCl2+1mM IDA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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