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- PDB-2kkf: Solution structure of MLL CXXC domain in complex with palindromic... -

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Basic information

Entry
Database: PDB / ID: 2kkf
TitleSolution structure of MLL CXXC domain in complex with palindromic CPG DNA
Components
  • 5'-D(*CP*CP*CP*TP*GP*CP*GP*CP*AP*GP*GP*G)-3'
  • Histone-lysine N-methyltransferase HRX
KeywordsDNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / CXXC DOMAIN / MLL / CPG DNA / CHROMOSOMAL REARRANGEMENT / DNA-BINDING / METAL-BINDING / NUCLEUS / ZINC-FINGER / DNA BINDING PROTEIN-DNA COMPLEX / Alternative splicing / Apoptosis / Bromodomain / Chromatin regulator / Isopeptide bond / Methyltransferase / Phosphoprotein / Polymorphism / Proto-oncogene / S-adenosyl-L-methionine / Transcription / Transcription regulation / Transferase / Ubl conjugation / Zinc
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 / regulation of short-term neuronal synaptic plasticity / exploration behavior / definitive hemopoiesis / histone H3K4 methyltransferase activity ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of short-term neuronal synaptic plasticity / exploration behavior / definitive hemopoiesis / histone H3K4 methyltransferase activity / T-helper 2 cell differentiation / embryonic hemopoiesis / anterior/posterior pattern specification / histone methyltransferase complex / : / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / MLL1 complex / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / epigenetic regulation of gene expression / spleen development / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / visual learning / circadian regulation of gene expression / protein modification process / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / fibroblast proliferation / protein-containing complex assembly / apoptotic process / chromatin binding / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / identical protein binding / cytosol
Similarity search - Function
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. ...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. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, DISTANCE GEOMETRY
Model detailslowest energy, model 1
AuthorsCierpicki, T. / Riesbeck, J.E. / Grembecka, J.E. / Lukasik, S.M. / Popovic, R. / Omonkowska, M. / Shultis, D.S. / Zeleznik-Le, N.J. / Bushweller, J.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structure of the MLL CXXC domain-DNA complex and its functional role in MLL-AF9 leukemia.
Authors: Cierpicki, T. / Risner, L.E. / Grembecka, J. / Lukasik, S.M. / Popovic, R. / Omonkowska, M. / Shultis, D.D. / Zeleznik-Le, N.J. / Bushweller, J.H.
History
DepositionJun 18, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: 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_struct_assembly / pdbx_struct_oper_list / struct_ref_seq / 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.db_align_beg / _struct_ref_seq.db_align_end / _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: Histone-lysine N-methyltransferase HRX
B: 5'-D(*CP*CP*CP*TP*GP*CP*GP*CP*AP*GP*GP*G)-3'
C: 5'-D(*CP*CP*CP*TP*GP*CP*GP*CP*AP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1385
Polymers14,0073
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone-lysine N-methyltransferase HRX / Zinc finger protein HRX / ALL-1 / Trithorax-like protein / Lysine N-methyltransferase 2A / CXXC- ...Zinc finger protein HRX / ALL-1 / Trithorax-like protein / Lysine N-methyltransferase 2A / CXXC-type zinc finger protein 7


Mass: 6677.991 Da / Num. of mol.: 1 / Fragment: CXXC DOMAIN: UNP RESIDUES 1147-1203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALL1, CXXC7, HRX, HTRX, KMT2A, MLL, TRX1 / Plasmid: pGEX4-T2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q03164, histone-lysine N-methyltransferase
#2: DNA chain 5'-D(*CP*CP*CP*TP*GP*CP*GP*CP*AP*GP*GP*G)-3'


Mass: 3664.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Palindromic DNA
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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 1H-15N NOESY
1213D 1H-13C NOESY
133HNCO NCO
143HNCO COCA
153HACAN
163IPAP
1742D 1H-13C HSQC NO DECOUPLING
1822D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 13C; U-98% 15N] CXXC domain-1, 1 mM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-2, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-98% 13C; U-98% 15N] CXXC domain-3, 1 mM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-4, 100% D2O100% D2O
31 mM [U-98% 13C; U-98% 15N] CXXC domain-5, 1 mM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-6, 95% H2O/5% D2O95% H2O/5% D2O
41 mM [U-98% 15N] CXXC domain-7, 1 mM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCXXC domain-1[U-98% 13C; U-98% 15N]1
1 mMDNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-21
1 mMCXXC domain-3[U-98% 13C; U-98% 15N]2
1 mMDNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-42
1 mMCXXC domain-5[U-98% 13C; U-98% 15N]3
1 mMDNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-63
1 mMCXXC domain-7[U-98% 15N]4
1 mMDNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-84
Sample conditionsIonic strength: 25 / pH: 7.0 / Pressure: Ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: VARIAN INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.11Goddardstructure solution
NMRPipe2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: SIMULATED ANNEALING, DISTANCE GEOMETRY / Software ordinal: 1
Details: HIGH TEMP ANNEALING WITHOUT RRDCS, LOW TEMP ANNEALING WITH RDCS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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