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- PDB-2jyi: Solution structure of MLL CXXC domain -

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Basic information

Entry
Database: PDB / ID: 2jyi
TitleSolution structure of MLL CXXC domain
ComponentsZinc finger protein HRX
KeywordsTRANSCRIPTION / PROTEIN / CXXC domain / MLL / Alternative splicing / Bromodomain / Chromosomal rearrangement / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Proto-oncogene / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger
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 / T-helper 2 cell differentiation / regulation of short-term neuronal synaptic plasticity / definitive hemopoiesis ...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 / T-helper 2 cell differentiation / regulation of short-term neuronal synaptic plasticity / definitive hemopoiesis / histone H3K4 methyltransferase activity / embryonic hemopoiesis / exploration behavior / 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 / spleen development / cellular response to transforming growth factor beta stimulus / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / circadian regulation of gene expression / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / protein modification process / visual learning / PKMTs methylate histone lysines / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / fibroblast proliferation / protein-containing complex assembly / methylation / chromatin binding / apoptotic process / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / 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 / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain profile. / SET domain / 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
Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, distance geometry
AuthorsCierpicki, T. / Bushweller, J.H.
CitationJournal: To be Published
Title: Structural basis for maintenance of unmethylated CpG elements by the CXXC domain of MLL and its critical contributions to MLL-AF9 immortalization activity
Authors: Cierpicki, T. / Riesbeck, L.E. / Grembecka, J. / Lukasik, S.M. / Omonkowska, M. / Shultis, D. / Zeleznik-Le, N.J. / Bushweller, J.H.
History
DepositionDec 13, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 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: Zinc finger protein HRX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6653
Polymers6,5341
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Zinc finger protein HRX / ALL-1 / Trithorax-like protein


Mass: 6533.862 Da / Num. of mol.: 1 / Fragment: CXXC domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLL, ALL1, HRX, HTRX, TRX1 / Plasmid: pGEX 4-T2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q03164
#2: 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
232IPAP
242HNCO NCo
252HNCO CoCa
363IPAP
373HNCO NCo
383HNCO CoCa

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 13C; U-98% 15N] CXXC, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-98% 13C; U-98% 15N] CXXC, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-98% 13C; U-98% 15N] CXXC, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCXXC[U-98% 13C; U-98% 15N]1
1 mMCXXC[U-98% 13C; U-98% 15N]2
1 mMCXXC[U-98% 13C; U-98% 15N]3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.37.1ambient atm298 K
20.37.1ambient atm298 K
30.37.1ambient atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddarddata analysis
Sparky3.11Goddardpeak picking
NMRPipe2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
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: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 14

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