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- PDB-2n1i: Structure of the PR domain from PRDM16 -

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Basic information

Entry
Database: PDB / ID: 2n1i
TitleStructure of the PR domain from PRDM16
ComponentsPR domain zinc finger protein 16
KeywordsTRANSCRIPTION / PR domain / PRDM16 / SET domain / HKMT / Lysine methyltransferase / MEL1
Function / homology
Function and homology information


histone H3K9 monomethyltransferase activity / negative regulation of granulocyte differentiation / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / regulation of cellular respiration / aggresome / histone H3 methyltransferase activity / heterochromatin organization / brown fat cell differentiation ...histone H3K9 monomethyltransferase activity / negative regulation of granulocyte differentiation / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / regulation of cellular respiration / aggresome / histone H3 methyltransferase activity / heterochromatin organization / brown fat cell differentiation / transcription repressor complex / transcription coregulator activity / negative regulation of transforming growth factor beta receptor signaling pathway / PKMTs methylate histone lysines / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of cold-induced thermogenesis / methylation / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription coactivator activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
PRDM16, PR/SET domain / PR domain zinc finger protein 2, PR domain / C2H2-type zinc finger / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain profile. / SET domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. ...PRDM16, PR/SET domain / PR domain zinc finger protein 2, PR domain / C2H2-type zinc finger / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain profile. / SET domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Histone-lysine N-methyltransferase PRDM16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsSun, Y. / Armstrong, G. / Briknarova, K.
CitationJournal: To be Published
Title: Structure of the PR Domain from PRDM16
Authors: Sun, Y. / Armstrong, G. / Briknarova, K.
History
DepositionApr 2, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PR domain zinc finger protein 16


Theoretical massNumber of molelcules
Total (without water)19,1701
Polymers19,1701
Non-polymers00
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 PR domain zinc finger protein 16 / PR domain-containing protein 16 / Transcription factor MEL1 / MDS1/EVI1-like gene 1


Mass: 19169.529 Da / Num. of mol.: 1 / Fragment: PR domain (UNP residues 54-226)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDM16, KIAA1675, MEL1, PFM13 / Plasmid: pDEST 15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q9HAZ2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HNCO
1813D HN(CA)CO
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D CCH-TOCSY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11412D HBCB(CGCD)HD
11523D 1H-15N NOESY
11632D DQF-COSY
11732D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.45-0.55 mM [U-99% 13C; U-99% 15N] PRDM16, 20 mM potassium phosphate, 50 mM potassium chloride, 2.5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.4-0.5 mM [U-99% 15N] PRDM16, 20 mM potassium phosphate, 50 mM potassium chloride, 2.5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM PRDM16, 20 mM potassium phosphate, 50 mM potassium chloride, 2.5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMPRDM16-1[U-99% 13C; U-99% 15N]0.45-0.551
20 mMpotassium phosphate-21
50 mMpotassium chloride-31
2.5 mMDTT-41
mMPRDM16-5[U-99% 15N]0.4-0.52
20 mMpotassium phosphate-62
50 mMpotassium chloride-72
2.5 mMDTT-82
0.5 mMPRDM16-93
20 mMpotassium phosphate-103
50 mMpotassium chloride-113
2.5 mMDTT-123
Sample conditionsIonic strength: 0.088 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Varian NMR SystemVarianVarian NMR System8001
Varian Varian NMR SystemVarianVarian NMR System9002
Varian Varian NMR SystemVarianVarian NMR System5003

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Processing

NMR software
NameDeveloperClassification
VnmrJAgilentcollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmrCCPNdata analysis
CcpNmrCCPNchemical shift assignment
CcpNmrCCPNpeak picking
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxgeneration of torsion angle restraints
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Cartesian dynamics and Powell minimization in explicit water (default Aria refinement protocol)
NMR constraintsNOE constraints total: 5181 / NOE intraresidue total count: 938 / NOE sequential total count: 1196 / Hydrogen bond constraints total count: 0 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 74 / Protein psi angle constraints total count: 74
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 6.73 ° / Maximum upper distance constraint violation: 0.469 Å
NMR ensemble rmsDistance rms dev: 0.0244 Å / Distance rms dev error: 0.00101 Å

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