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- PDB-2j2s: Solution structure of the nonmethyl-CpG-binding CXXC domain of th... -

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Basic information

Entry
Database: PDB / ID: 2j2s
TitleSolution structure of the nonmethyl-CpG-binding CXXC domain of the leukaemia-associated MLL histone methyltransferase
ComponentsZINC FINGER PROTEIN HRX
KeywordsTRANSCRIPTION REGULATION / CHROMOSOMAL REARRANGEMENT / ZINC-FINGER / DNA-BINDING / BROMODOMAIN / POLYMORPHISM / MIXED LINEAGE LEUKAEMIA / ZINC BINDING / TRANSCRIPTION / METAL-BINDING / ZINC / CXXC / MBD1 / HOX GENES / CHROMATIN / METHYLATION / PROTO-ONCOGENE / NUCLEAR PROTEIN / PHOSPHORYLATION / CPG DINUCLEOTIDE / ALTERNATIVE SPLICING
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 / regulation of short-term neuronal synaptic plasticity / T-helper 2 cell differentiation / 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 / regulation of short-term neuronal synaptic plasticity / T-helper 2 cell differentiation / 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 / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / 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 / visual learning / protein modification process / PKMTs methylate histone lysines / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / fibroblast proliferation / methylation / 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 / 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 / CNS
AuthorsAllen, M.D. / Grummitt, C.G. / Hilcenko, C. / Young-Min, S. / Tonkin, L.M. / Johnson, C.M. / Bycroft, M. / Warren, A.J.
CitationJournal: Embo J. / Year: 2006
Title: Solution Structure of the Nonmethyl-Cpg-Binding Cxxc Domain of the Leukaemia-Associated Mll Histone Methyltransferase
Authors: Allen, M.D. / Grummitt, C.G. / Hilcenko, C. / Min, S.Y. / Tonkin, L.M. / Johnson, C.M. / Freund, S.M. / Bycroft, M. / Warren, A.J.
History
DepositionAug 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Other
Revision 1.2May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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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)8,1973
Polymers8,0671
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)20 / 20NO VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein ZINC FINGER PROTEIN HRX / ALL-1 / TRITHORAX-LIKE PROTEIN / CXXC DOMAIN OF MLL-1


Mass: 8066.666 Da / Num. of mol.: 1 / Fragment: RESIDUES 1146-1214 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER / References: UniProt: Q03164
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 1143 TO GLY ENGINEERED RESIDUE IN CHAIN A, PRO 1144 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, GLU 1143 TO GLY ENGINEERED RESIDUE IN CHAIN A, PRO 1144 TO GLY ENGINEERED RESIDUE IN CHAIN A, PRO 1145 TO SER
Sequence detailsMUTATIONS AT THE N-TERMINUS ARE REQUIRED FOR REMOVAL OF FUSION PROTEIN. GLY 1143-SER 1145 REQUIRED ...MUTATIONS AT THE N-TERMINUS ARE REQUIRED FOR REMOVAL OF FUSION PROTEIN. GLY 1143-SER 1145 REQUIRED FOR PURIFICATION.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED CXXC DOMAIN

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Sample preparation

DetailsContents: 90% WATER, 10% D2O
Sample conditionspH: 6.5 / Temperature: 290.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
ANSIGstructure solution
RefinementMethod: CNS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: NO VIOLATIONS / Conformers calculated total number: 20 / Conformers submitted total number: 20

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