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- PDB-5lv5: Crystal structure of mouse PRMT6 in complex with inhibitor LH1458 -

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Basic information

Entry
Database: PDB / ID: 5lv5
TitleCrystal structure of mouse PRMT6 in complex with inhibitor LH1458
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 / RMTs methylate histone arginines / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase / histone H4R3 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 / RMTs methylate histone arginines / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase / histone H4R3 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 / 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 ...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-78G / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,1472
Polymers44,5971
Non-polymers5501
Water3,981221
1
A: Protein arginine N-methyltransferase 6
hetero molecules

A: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2934
Polymers89,1942
Non-polymers1,0992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area3240 Å2
ΔGint-32 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.703, 77.703, 117.692
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-78G / 2-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethyl-[[4-azanyl-1-(methoxymethyl)-2-oxidanylidene-pyrimidin-5-yl]methyl]-[(3~{S})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]azanium


Mass: 549.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H33N10O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.99 Å3/Da / Density % sol: 38.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris-HCl 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 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.8→40.16 Å / Num. obs: 32113 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 23.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.261 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.421 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.11rc1_2513: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C07

4c07


Resolution: 1.802→40.16 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 1607 5.01 %Random selection
Rwork0.154 ---
obs0.1561 32094 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.802→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 39 221 2762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012633
X-RAY DIFFRACTIONf_angle_d1.063577
X-RAY DIFFRACTIONf_dihedral_angle_d16.592986
X-RAY DIFFRACTIONf_chiral_restr0.08395
X-RAY DIFFRACTIONf_plane_restr0.007481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8025-1.86070.34041470.27592721X-RAY DIFFRACTION98
1.8607-1.92720.23021470.22472776X-RAY DIFFRACTION100
1.9272-2.00430.23041410.18122784X-RAY DIFFRACTION100
2.0043-2.09550.21651470.16432768X-RAY DIFFRACTION100
2.0955-2.2060.21151500.15122743X-RAY DIFFRACTION100
2.206-2.34420.18581460.14492773X-RAY DIFFRACTION100
2.3442-2.52520.18461410.14562787X-RAY DIFFRACTION100
2.5252-2.77930.18871450.14812784X-RAY DIFFRACTION100
2.7793-3.18130.19071470.15762758X-RAY DIFFRACTION100
3.1813-4.00750.1711470.13662780X-RAY DIFFRACTION100
4.0075-40.170.1861490.14232813X-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)
11.0468-0.21520.52250.8798-0.08140.8650.05260.0916-0.0883-0.0051-0.07610.07890.0281-0.0389-0.00810.03840.00460.02070.0773-0.00290.069514.3788-14.24255.3231
20.21680.0826-0.038-0.10020.1037-0.11620.07190.0816-0.03590.05450.02530.03770.04590.0250.00210.1201-0.0046-0.0040.2433-0.00040.170139.352817.226113.2777
30.46030.0032-0.09081.5871-0.00260.91020.0525-0.00210.0597-0.0191-0.03360.0123-0.08240.003-0.00040.11810.00110.0030.14840.01210.125119.902112.30898.7829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 190 )
2X-RAY DIFFRACTION2chain 'A' and (resid 191 through 234 )
3X-RAY DIFFRACTION3chain 'A' and (resid 235 through 377 )

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