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- PDB-2lv9: Solution NMR structure of the PHD domain of human MLL5, Northeast... -

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Basic information

Entry
Database: PDB / ID: 2lv9
TitleSolution NMR structure of the PHD domain of human MLL5, Northeast structural genomics consortium target HR6512A
ComponentsHistone-lysine N-methyltransferase MLL5
KeywordsTRANSFERASE / Zinc Finger / transcription / protein binding / NESG / Northeast structural genomics consortium / SGC / Structural Genomics Consortium / PSI-Biology / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes / CEBS
Function / homology
Function and homology information


Set3 complex / Rpd3L-Expanded complex / neutrophil activation / neutrophil mediated immunity / positive regulation of G1/S transition of mitotic cell cycle / epigenetic regulation of gene expression / methylated histone binding / erythrocyte differentiation / euchromatin / transcription coactivator activity ...Set3 complex / Rpd3L-Expanded complex / neutrophil activation / neutrophil mediated immunity / positive regulation of G1/S transition of mitotic cell cycle / epigenetic regulation of gene expression / methylated histone binding / erythrocyte differentiation / euchromatin / transcription coactivator activity / nuclear body / nuclear speck / cell cycle / centrosome / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
KMT2E, SET domain / PhD finger domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / SET domain / SET domain profile. / SET domain / Herpes Virus-1 / Zinc finger, PHD-type, conserved site ...KMT2E, SET domain / PhD finger domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / SET domain / SET domain profile. / SET domain / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / 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 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Inactive histone-lysine N-methyltransferase 2E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / restrained molecular dynamics
Model detailslowest energy, model 1
AuthorsLemak, A. / Yee, A. / Houliston, S. / Garcia, M. / Wu, H. / Min, J. / Montelione, G.T. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG) / Structural Genomics Consortium (SGC) / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes (CEBS)
CitationJournal: To be Published
Title: NMR solution structure of the human MLL5 PHD domain (CASP Target)
Authors: Lemak, A. / Yee, A. / Houliston, S. / Garcia, M. / Wu, H. / Min, J. / Montelione, G.T. / Arrowsmith, C.
History
DepositionJun 29, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Structure summary
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase MLL5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6503
Polymers11,5191
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone-lysine N-methyltransferase MLL5 / Lysine N-methyltransferase 2E / KMT2E / Myeloid/lymphoid or mixed-lineage leukemia protein 5


Mass: 11518.857 Da / Num. of mol.: 1 / Fragment: PHD-type domain residues 109-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLL5, KMT2E / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IZD2, histone-lysine N-methyltransferase
#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 HNCO
1213D HNCA
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D (H)CCH-TOCSY
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] protein, 10 mM TRIS, 300 mM sodium chloride, 10 uM ZnSO4, 1 mM DTT, 0.01 % NaN3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-13C; U-15N]1
10 mMTRIS-21
300 mMsodium chloride-31
10 uMZnSO4-41
1 mMDTT-51
0.01 %NaN3-61
Sample conditionsIonic strength: 300 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FMCLemak,Steren,Llinas, Arrowsmithchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
PSVSBhattacharya and Montelionevalidation
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: restrained 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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