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- PDB-4y2h: Crystal structure of human protein arginine methyltransferase PRM... -

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Basic information

Entry
Database: PDB / ID: 4y2h
TitleCrystal structure of human protein arginine methyltransferase PRMT6 bound to SAH and an aryl pyrazole inhibitor
ComponentsProtein arginine N-methyltransferase 6
KeywordsTRANSFERASE
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H3R2 methyltransferase activity / histone H4R3 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H3R2 methyltransferase activity / histone H4R3 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone H3 methyltransferase activity / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / base-excision repair / protein modification process / RMTs methylate histone arginines / cellular senescence / histone binding / methylation / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Arginine methyltransferase oligomerization subdomain / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Arginine methyltransferase oligomerization subdomain / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-49K / S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.37 Å
AuthorsSwinger, K.K. / Boriack-Sjodin, P.A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2015
Title: Aryl Pyrazoles as Potent Inhibitors of Arginine Methyltransferases: Identification of the First PRMT6 Tool Compound.
Authors: Mitchell, L.H. / Drew, A.E. / Ribich, S.A. / Rioux, N. / Swinger, K.K. / Jacques, S.L. / Lingaraj, T. / Boriack-Sjodin, P.A. / Waters, N.J. / Wigle, T.J. / Moradei, O. / Jin, L. / Riera, T. ...Authors: Mitchell, L.H. / Drew, A.E. / Ribich, S.A. / Rioux, N. / Swinger, K.K. / Jacques, S.L. / Lingaraj, T. / Boriack-Sjodin, P.A. / Waters, N.J. / Wigle, T.J. / Moradei, O. / Jin, L. / Riera, T. / Porter-Scott, M. / Moyer, M.P. / Smith, J.J. / Chesworth, R. / Copeland, R.A.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 6
B: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6077
Polymers79,2502
Non-polymers1,3585
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-31 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.970, 99.970, 89.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Protein arginine N-methyltransferase 6 / Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 6 / Histone-arginine N- ...Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 6 / Histone-arginine N-methyltransferase PRMT6


Mass: 39624.992 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT6, HRMT1L6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96LA8, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: 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
#3: Chemical ChemComp-49K / N-{[5-(4-fluorophenyl)-1H-pyrazol-4-yl]methyl}-N-methylethane-1,2-diamine


Mass: 248.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17FN4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: MgCl, MES buffer pH 6.5, Isopropanol, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97856 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.37→27.74 Å / Num. obs: 35874 / % possible obs: 99.9 % / Redundancy: 4.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.073 / Net I/σ(I): 10.5 / Num. measured all: 175169
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.37-2.433.50.5942.2927926420.6650.37199.8
10.6-27.744.60.03628.918674060.9980.01895

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Aimless0.1.28data scaling
PDB_EXTRACT3.15data extraction
XDSdata scaling
REFMACphasing
RefinementResolution: 2.37→27.74 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.754 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 1794 5 %RANDOM
Rwork0.1817 34051 --
obs0.1842 34050 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.25 Å2 / Biso mean: 23.621 Å2 / Biso min: 6.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 2.37→27.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5452 0 94 262 5808
Biso mean--16.95 25.94 -
Num. residues----689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195688
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9757711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0145691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05823.086269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57715945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1041554
X-RAY DIFFRACTIONr_chiral_restr0.0940.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214362
X-RAY DIFFRACTIONr_mcbond_it1.2772.2182770
X-RAY DIFFRACTIONr_mcangle_it2.2023.3213459
X-RAY DIFFRACTIONr_scbond_it1.8712.4252918
LS refinement shellResolution: 2.37→2.431 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 137 -
Rwork0.247 2489 -
all-2626 -
obs--99.81 %

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