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- PDB-2g46: structure of vSET in complex with meK27 H3 Pept. and cofactor pro... -

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Basic information

Entry
Database: PDB / ID: 2g46
Titlestructure of vSET in complex with meK27 H3 Pept. and cofactor product SAH
Components
  • PBCV-1 histone H3-Lys 27 methyltransferase
  • meK27 H3 Peptide
KeywordsTRANSFERASE / vSET structure / hsitone methyltransferase
Function / homology
Function and homology information


histone H3K37 methyltransferase activity / nucleosome / methylation / protein heterodimerization activity / DNA binding / identical protein binding
Similarity search - Function
Histone-lysine N-methyltransferase, H3 lysine-37 specific / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Histone H3 signature 1. ...Histone-lysine N-methyltransferase, H3 lysine-37 specific / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Histone H3 signature 1. / Histone H3/CENP-A / Histone-fold / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / : / Histone H3 / Histone H3K27 methylase
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
AuthorsQian, C.M. / Zheng, L. / Zhou, M.M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural insights of the specificity and catalysis of a viral histone H3 lysine 27 methyltransferase.
Authors: Qian, C.M. / Wang, X. / Manzur, K. / Sachchidanand / Farooq, A. / Zeng, L. / Wang, R. / Zhou, M.M.
History
DepositionFeb 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: PBCV-1 histone H3-Lys 27 methyltransferase
C: meK27 H3 Peptide
B: PBCV-1 histone H3-Lys 27 methyltransferase
D: meK27 H3 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2376
Polymers31,4684
Non-polymers7692
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PBCV-1 histone H3-Lys 27 methyltransferase / vSET


Mass: 13606.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Genus: Chlorovirus / Gene: A612L / Plasmid: PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 9632146, UniProt: O41094*PLUS
#2: Protein/peptide meK27 H3 Peptide


Mass: 2127.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: O24165*PLUS
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
121HNHA
131HN(CO)CA,HN(CA)CB,HN(CO)CACB
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 0.5 mM protein with 2.5 mM meK27 H3 Pept. and 2.5mM SAH
Solvent system: in a 50 mM phosphate buffer of pH 6.5 containing 700 mM NaCl, 300 mM urea, 0.1 mM EDTA and 5 mM -ME in H2O/2H2O (9/1) or 2H2O
Sample conditionsIonic strength: 300mM NaCl and 700mM Urea / pH: 6.5 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE7503

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerrefinement
NMRPipeBax ADprocessing
ARIA1.2Nigles M.refinement
NMRView5Bruce A. Johnsondata analysis
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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