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- PDB-5lv4: Crystal structure of mouse PRMT6 in complex with inhibitor LH1236 -

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Basic information

Entry
Database: PDB / ID: 5lv4
TitleCrystal structure of mouse PRMT6 in complex with inhibitor LH1236
ComponentsProtein arginine N-methyltransferase 6
KeywordsTRANSFERASE / S-ADENOSYL-L-METHIONINE
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H3R2 methyltransferase activity / histone H4R3 methyltransferase activity / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H3R2 methyltransferase activity / histone H4R3 methyltransferase activity / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / protein modification process / cellular senescence / histone binding / methylation / chromatin remodeling / DNA repair / 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-78K / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsCura, V. / Marechal, N. / Troffer-Charlier, N. / Halby, L. / Arimondo, P. / Bonnefond, L. / Cavarelli, J.
CitationJournal: Philos. Trans. R. Soc. Lond., B, Biol. Sci. / Year: 2018
Title: Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors.
Authors: Halby, L. / Marechal, N. / Pechalrieu, D. / Cura, V. / Franchini, D.M. / Faux, C. / Alby, F. / Troffer-Charlier, N. / Kudithipudi, S. / Jeltsch, A. / Aouadi, W. / Decroly, E. / Guillemot, J. ...Authors: Halby, L. / Marechal, N. / Pechalrieu, D. / Cura, V. / Franchini, D.M. / Faux, C. / Alby, F. / Troffer-Charlier, N. / Kudithipudi, S. / Jeltsch, A. / Aouadi, W. / Decroly, E. / Guillemot, J.C. / Page, P. / Ferroud, C. / Bonnefond, L. / Guianvarc'h, D. / Cavarelli, J. / Arimondo, P.B.
History
DepositionSep 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1322
Polymers44,5971
Non-polymers5351
Water5,963331
1
A: Protein arginine N-methyltransferase 6
hetero molecules

A: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2634
Polymers89,1942
Non-polymers1,0692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area3240 Å2
ΔGint-33 kcal/mol
Surface area26630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.851, 79.851, 119.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Protein arginine N-methyltransferase 6 / Histone-arginine N-methyltransferase PRMT6


Mass: 44597.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prmt6, Hrmt1l6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6NZB1, type I protein arginine methyltransferase
#2: Chemical ChemComp-78K / (2~{R})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[[4-azanyl-1-(methoxymethyl)-2-oxidanylidene-pyrimidin-5-yl]methyl]amino]-2-azanyl-butanoic acid


Mass: 534.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: HEPES NaOH pH 8.0 100 mM PEG 6000 10 % MgCl2 200 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 1.66→41.08 Å / Num. obs: 44207 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 21.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.142 / Net I/σ(I): 7.7
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.508 / Mean I/σ(I) obs: 1 / CC1/2: 0.474 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C07

4c07


Resolution: 1.66→41.08 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / Phase error: 19.85
RfactorNum. reflection% reflectionSelection details
Rfree0.1882 2209 5 %Random selection
Rwork0.1585 ---
obs0.16 44183 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 1.66→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 38 331 2857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092604
X-RAY DIFFRACTIONf_angle_d1.0793540
X-RAY DIFFRACTIONf_dihedral_angle_d21.929978
X-RAY DIFFRACTIONf_chiral_restr0.093391
X-RAY DIFFRACTIONf_plane_restr0.007476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.658-1.69410.31091340.28852506X-RAY DIFFRACTION96
1.6941-1.73350.28021370.26162604X-RAY DIFFRACTION100
1.7335-1.77680.28151410.24142659X-RAY DIFFRACTION100
1.7768-1.82490.28451340.222612X-RAY DIFFRACTION100
1.8249-1.87860.23321410.21572632X-RAY DIFFRACTION100
1.8786-1.93920.20371370.19482633X-RAY DIFFRACTION100
1.9392-2.00850.191340.17562607X-RAY DIFFRACTION100
2.0085-2.08890.23121410.16152630X-RAY DIFFRACTION100
2.0889-2.1840.19281390.15822630X-RAY DIFFRACTION100
2.184-2.29910.18151360.14852606X-RAY DIFFRACTION100
2.2991-2.44320.1851390.15322646X-RAY DIFFRACTION100
2.4432-2.63180.17271390.14262623X-RAY DIFFRACTION100
2.6318-2.89660.18241390.14982647X-RAY DIFFRACTION100
2.8966-3.31550.18191380.15162649X-RAY DIFFRACTION100
3.3155-4.17660.16561390.13532616X-RAY DIFFRACTION100
4.1766-41.08940.16081410.14192674X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.976-0.42130.4070.658-0.64951.18490.0843-0.0141-0.1559-0.00750.00140.02770.168-0.09810.00010.1591-0.02790.00580.17230.00520.17416.4289-18.07896.2575
20.3858-0.1399-0.29350.34970.10730.33550.0660.09430.0003-0.0504-0.1030.0569-0.0413-0.0961-0.00010.14580.01370.00090.21780.00990.192713.9636-2.11894.4011
30.70180.0245-0.0038-0.09970.1555-0.10730.13330.01840.09660.1398-0.04770.03740.0380.000700.2123-0.00510.00980.24660.01530.214340.241516.551812.9866
40.18650.0488-0.22170.0467-0.00550.2554-0.0030.09770.147-0.12250.15250.2681-0.1961-0.14610.04190.20050.0203-0.01020.25030.04180.270710.18199.75174.7072
50.4741-0.0957-0.33350.414800.63350.155-0.07810.02690.2463-0.0891-0.0438-0.07140.07290.00030.1873-0.01560.01990.18880.00720.187723.251911.106414.7605
60.20990.21610.04820.434-0.48530.81380.17420.13150.1082-0.1892-0.0687-0.0518-0.0157-0.0560.00370.21770.0190.03940.20470.04480.216322.382316.35631.169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 153 )
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 202 )
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 253 )
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 281 )
5X-RAY DIFFRACTION5chain 'A' and (resid 282 through 338 )
6X-RAY DIFFRACTION6chain 'A' and (resid 339 through 378 )

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