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- PDB-2ku7: Solution structure of MLL1 PHD3-Cyp33 RRM chimeric protein -

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Entry
Database: PDB / ID: 2ku7
TitleSolution structure of MLL1 PHD3-Cyp33 RRM chimeric protein
ComponentsMLL1 PHD3-Cyp33 RRM chimeric protein
KeywordsTRANSCRIPTION / MLL1 / Cyp33 / transcriptional regulation / RRM domain
Function / homology
Function and homology information


protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / poly(A) binding / regulation of short-term neuronal synaptic plasticity / T-helper 2 cell differentiation ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / poly(A) binding / regulation of short-term neuronal synaptic plasticity / T-helper 2 cell differentiation / definitive hemopoiesis / histone H3K4 methyltransferase activity / U2-type catalytic step 2 spliceosome / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / histone methyltransferase complex / cyclosporin A binding / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / MLL1 complex / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / spleen development / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / circadian regulation of gene expression / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / PKMTs methylate histone lysines / mRNA splicing, via spliceosome / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Transcriptional regulation of granulopoiesis / protein folding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / fibroblast proliferation / methylation / protein-containing complex assembly / secretory granule lumen / ficolin-1-rich granule lumen / nuclear speck / intracellular membrane-bounded organelle / mRNA binding / apoptotic process / chromatin binding / Neutrophil degranulation / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus ...Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / 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. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / 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 / RRM (RNA recognition motif) domain / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Zinc finger, PHD-type / PHD zinc finger / RNA-binding domain superfamily / Zinc finger, FYVE/PHD-type / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase 2A / Peptidyl-prolyl cis-trans isomerase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsSong, J. / Wang, Z. / Patel, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Pro isomerization in MLL1 PHD3-bromo cassette connects H3K4me readout to CyP33 and HDAC-mediated repression.
Authors: Wang, Z. / Song, J. / Milne, T.A. / Wang, G.G. / Li, H. / Allis, C.D. / Patel, D.J.
History
DepositionFeb 12, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MLL1 PHD3-Cyp33 RRM chimeric protein


Theoretical massNumber of molelcules
Total (without water)15,2581
Polymers15,2581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein MLL1 PHD3-Cyp33 RRM chimeric protein


Mass: 15257.954 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03164, UniProt: Q9UNP9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HBHA(CO)NH
1613D (H)CCH-TOCSY
1713D 15N-edited 1H-1H NOESY
1813D 13C-edited 1H-1H NOESY
1913D HNCO

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Sample preparation

DetailsContents: 0.3-0.5 mM [U-100% 13C; U-100% 15N] MLL PHD3-Cyp33 RRM, 20 mM sodium phosphate, 50 mM sodium chloride, 0.4 mM DSS, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMMLL PHD3-Cyp33 RRM[U-100% 13C; U-100% 15N]0.3-0.51
20 mMsodium phosphate-1
50 mMsodium chloride-1
0.4 mMDSS1
Sample conditionsIonic strength: 50 / pH: 7.0 / Pressure: ambient / Temperature: 298.2 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, F. et al.processing
SparkyGoddard, T. et al.data analysis
SparkyGoddard, T. et al.peak picking
CYANAGuntert, P. et al.structure solution
X-PLOR NIHSchwieters, C. et al.structure solution
X-PLOR NIHSchwieters, C. et al.refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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