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- PDB-4y30: Crystal structure of human protein arginine methyltransferase PRM... -

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Basic information

Entry
Database: PDB / ID: 4y30
TitleCrystal structure of human protein arginine methyltransferase PRMT6 bound to SAH and EPZ020411
ComponentsProtein arginine N-methyltransferase 6
KeywordsTRANSFERASE
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 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 ...histone H2AR3 methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 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 / base-excision repair / protein modification process / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / cellular senescence / histone binding / 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 / 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 ...Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / 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-49L / S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)81,00410
Polymers79,0502
Non-polymers1,9558
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-36 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.672, 99.672, 89.252
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 39 - 374 / Label seq-ID: 15 - 350

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#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: 39524.836 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-375
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

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Non-polymers , 5 types, 522 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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-49L / N,N'-dimethyl-N-({3-[4-({trans-3-[2-(tetrahydro-2H-pyran-4-yl)ethoxy]cyclobutyl}oxy)phenyl]-1H-pyrazol-4-yl}methyl)ethane-1,2-diamine


Mass: 442.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H38N4O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
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: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→99.67 Å / Num. obs: 50960 / % possible obs: 99.8 % / Redundancy: 5 % / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
REFMACphasing
RefinementResolution: 2.1→43.51 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.729 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 2420 4.8 %RANDOM
Rwork0.1799 48520 --
obs0.1818 50960 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.74 Å2 / Biso mean: 17.88 Å2 / Biso min: 4.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å20 Å2
2--0.22 Å2-0 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 2.1→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5445 0 135 515 6095
Biso mean--19.93 26.64 -
Num. residues----688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195827
X-RAY DIFFRACTIONr_bond_other_d0.0040.025501
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9797906
X-RAY DIFFRACTIONr_angle_other_deg0.996312642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08822.971276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84915966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.381558
X-RAY DIFFRACTIONr_chiral_restr0.0720.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026607
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021389
X-RAY DIFFRACTIONr_mcbond_it1.1761.5982822
X-RAY DIFFRACTIONr_mcbond_other1.1761.5972823
X-RAY DIFFRACTIONr_mcangle_it2.032.3883540
Refine LS restraints NCS

Ens-ID: 1 / Number: 19680 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 183 -
Rwork0.229 3540 -
all-3723 -
obs--98.99 %

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