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- PDB-6emq: Solution structure of the LEDGF/p75 IBD - MLL1 (aa 111-160) complex -

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Basic information

Entry
Database: PDB / ID: 6emq
TitleSolution structure of the LEDGF/p75 IBD - MLL1 (aa 111-160) complex
ComponentsPC4 and SFRS1-interacting protein,Histone-lysine N-methyltransferase 2A
KeywordsTRANSCRIPTION / protein-protein complex / epigenetics / leukemia
Function / homology
Function and homology information


negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of short-term neuronal synaptic plasticity / definitive hemopoiesis / histone H3K4 methyltransferase activity ...negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of short-term neuronal synaptic plasticity / definitive hemopoiesis / histone H3K4 methyltransferase activity / supercoiled DNA binding / embryonic hemopoiesis / T-helper 2 cell differentiation / exploration behavior / anterior/posterior pattern specification / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / histone methyltransferase complex / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / mRNA 5'-splice site recognition / APOBEC3G mediated resistance to HIV-1 infection / minor groove of adenine-thymine-rich DNA binding / MLL1 complex / membrane depolarization / heterochromatin / negative regulation of fibroblast proliferation / spleen development / cellular response to transforming growth factor beta stimulus / homeostasis of number of cells within a tissue / transcription initiation-coupled chromatin remodeling / nuclear periphery / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / lysine-acetylated histone binding / circadian regulation of gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / euchromatin / visual learning / protein modification process / PKMTs methylate histone lysines / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to heat / protein-containing complex assembly / fibroblast proliferation / DNA-binding transcription factor binding / methylation / response to oxidative stress / transcription coactivator activity / chromatin remodeling / apoptotic process / chromatin binding / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / RNA binding / 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 / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Cysteine-rich motif following a subset of SET domains / TFIIS/LEDGF domain superfamily / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain / SET domain superfamily / SET domain profile. / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP 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
PC4 and SFRS1-interacting protein / Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsVeverka, V.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Affinity switching of the LEDGF/p75 IBD interactome is governed by kinase-dependent phosphorylation.
Authors: Sharma, S. / Cermakova, K. / De Rijck, J. / Demeulemeester, J. / Fabry, M. / El Ashkar, S. / Van Belle, S. / Lepsik, M. / Tesina, P. / Duchoslav, V. / Novak, P. / Hubalek, M. / Srb, P. / ...Authors: Sharma, S. / Cermakova, K. / De Rijck, J. / Demeulemeester, J. / Fabry, M. / El Ashkar, S. / Van Belle, S. / Lepsik, M. / Tesina, P. / Duchoslav, V. / Novak, P. / Hubalek, M. / Srb, P. / Christ, F. / Rezacova, P. / Hodges, H.C. / Debyser, Z. / Veverka, V.
History
DepositionOct 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: PC4 and SFRS1-interacting protein,Histone-lysine N-methyltransferase 2A


Theoretical massNumber of molelcules
Total (without water)17,9631
Polymers17,9631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12330 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein PC4 and SFRS1-interacting protein,Histone-lysine N-methyltransferase 2A / CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived ...CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52 / Lysine N-methyltransferase 2A / ALL-1 / CXXC-type zinc finger protein 7 / Myeloid/lymphoid or mixed-lineage leukemia / Myeloid/lymphoid or mixed-lineage leukemia protein 1 / Trithorax-like protein / Zinc finger protein HRX


Mass: 17963.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: PSIP1, DFS70, LEDGF, PSIP2, KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1
Production host: Escherichia coli (E. coli)
References: UniProt: O75475, UniProt: Q03164, histone-lysine N-methyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D HNCO
131isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-MLL1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O
Label: s1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLEDGF/p75 IBD-MLL1[U-13C; U-15N]1
50 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 200 mM / Label: c1 / pH: 7 / Pressure: arbitrary Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
YASARAKRIEGERrefinement
TopSpinstructure solution
Sparkystructure solution
CYANAstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 40

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