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- PDB-7ppy: CARM1 in complex with EML709 -

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Basic information

Entry
Database: PDB / ID: 7ppy
TitleCARM1 in complex with EML709
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSCRIPTION / protein arginine N-methyltransferase / PRMT4 / CARM1 / inhibitor
Function / homology
Function and homology information


histone H3R26 methyltransferase activity / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / type I protein arginine methyltransferase / negative regulation of dendrite development / protein-arginine omega-N asymmetric methyltransferase activity ...histone H3R26 methyltransferase activity / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / type I protein arginine methyltransferase / negative regulation of dendrite development / protein-arginine omega-N asymmetric methyltransferase activity / Cytoprotection by HMOX1 / protein methyltransferase activity / Estrogen-dependent gene expression / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / histone methyltransferase activity / nuclear replication fork / positive regulation of fat cell differentiation / nuclear receptor-mediated steroid hormone signaling pathway / response to cAMP / protein localization to chromatin / estrogen receptor signaling pathway / nuclear receptor coactivator activity / lysine-acetylated histone binding / RNA polymerase II transcription regulator complex / methylation / cell population proliferation / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / positive regulation of cell population proliferation / regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleus / cytosol
Similarity search - Function
Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-7ZH / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsMarechal, N. / Cura, V. / Bonnefond, L. / Troffer-Charlier, N. / Cavarelli, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction- ...Title: Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction-Reconstruction and Fragment-Growing Approach.
Authors: Iannelli, G. / Milite, C. / Marechal, N. / Cura, V. / Bonnefond, L. / Troffer-Charlier, N. / Feoli, A. / Rescigno, D. / Wang, Y. / Cipriano, A. / Viviano, M. / Bedford, M.T. / Cavarelli, J. ...Authors: Iannelli, G. / Milite, C. / Marechal, N. / Cura, V. / Bonnefond, L. / Troffer-Charlier, N. / Feoli, A. / Rescigno, D. / Wang, Y. / Cipriano, A. / Viviano, M. / Bedford, M.T. / Cavarelli, J. / Castellano, S. / Sbardella, G.
History
DepositionSep 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,63720
Polymers163,4024
Non-polymers3,23516
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.677, 98.823, 206.981
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Histone-arginine methyltransferase CARM1 / Coactivator-associated arginine methyltransferase 1 / Protein arginine N-methyltransferase 4


Mass: 40850.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Carm1, Prmt4
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9WVG6, type I protein arginine methyltransferase
#2: Chemical
ChemComp-7ZH / methyl 6-[4-[[~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]carbamimidoyl]amino]butylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate


Mass: 622.632 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H34N10O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 12% PEG 2000, 100mM NaCl, 100mM TrisHCl pH8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.42→48.06 Å / Num. obs: 58136 / % possible obs: 98.3 % / Redundancy: 4.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.062 / Rrim(I) all: 0.131 / Net I/σ(I): 8.8
Reflection shellResolution: 2.42→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3623 / CC1/2: 0.441 / Rpim(I) all: 0.743 / Rrim(I) all: 1.441 / % possible all: 80

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3


Resolution: 2.42→48.06 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 2875 4.96 %
Rwork0.2055 55124 -
obs0.207 57999 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.07 Å2 / Biso mean: 54.5883 Å2 / Biso min: 28.71 Å2
Refinement stepCycle: final / Resolution: 2.42→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10971 0 436 104 11511
Biso mean--67.01 46.85 -
Num. residues----1368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.42-2.460.3898960.35711779187568
2.46-2.50.34451230.32962599272299
2.5-2.550.32451360.307226322768100
2.55-2.60.30831370.298926602797100
2.6-2.650.35281410.288426302771100
2.65-2.710.29161360.26326262762100
2.71-2.770.32541220.259726642786100
2.77-2.840.3311420.267726432785100
2.84-2.920.32051360.263426202756100
2.92-3.010.26591340.258126702804100
3.01-3.10.25551470.24032640278799
3.1-3.210.2971430.23426302773100
3.21-3.340.26241340.233426612795100
3.34-3.490.23221190.217126802799100
3.49-3.680.23181320.195226662798100
3.68-3.910.22251630.179426682831100
3.91-4.210.20411450.161426572802100
4.21-4.630.16551420.14332691283399
4.63-5.30.18231320.143527242856100
5.3-6.680.19881520.18727452897100
6.68-48.060.18841630.18042839300298
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)
11.9239-0.4863-0.25022.84670.3242.95450.1148-0.15070.14940.1585-0.08570.0902-0.3153-0.0034-0.00630.3366-0.06360.05430.3291-0.03530.354255.048740.4899133.2064
22.05630.9310.39170.55040.19641.0950.2057-0.055-0.09750.1609-0.1196-0.09260.00540.0464-0.0870.28220.00220.01010.2992-0.01320.404645.970211.9832117.7019
30.77110.414-0.62961.89111.24341.0504-0.09640.0925-0.07380.05820.0423-0.15210.05460.06780.00580.3179-0.06540.03430.39830.00480.452861.349320.4498122.2938
40.76990.6626-0.13312.9865-0.00281.9121-0.0337-0.0626-0.0311-0.14630.0322-0.13920.15010.21340.0330.2019-0.03620.04270.353-0.00510.321961.917218.5787120.8368
51.73290.87290.192.1559-0.3131.24310.0918-0.10430.00150.0097-0.08250.22910.0087-0.256-0.11420.4214-0.01950.06450.4477-0.02730.39653.21417.0856114.4022
62.2544-0.2309-0.63272.35280.9033.56590.15680.13290.2159-0.0671-0.01580.1317-0.3452-0.1095-0.15760.31790.07910.02440.29410.04730.363319.74819.8303114.4774
71.53690.9527-0.56920.5259-0.08490.04190.3362-0.49840.17360.2383-0.28690.11830.06380.1275-0.06850.51270.01390.06520.4456-0.00730.389833.08128.0406144.0689
81.9941-0.31560.07431.07140.81211.81410.109-0.23130.11930.1099-0.05290.09270.2333-0.3173-0.03930.421-0.01160.06330.48550.04740.453617.39622.2206137.9105
92.02050.4080.61651.19081.06432.27150.2168-0.344-0.05120.1857-0.0562-0.05110.0361-0.0589-0.09610.39050.02310.05450.46360.08230.364717.267123.01140.1898
100.9280.19750.79620.98650.30121.57290.1542-0.1386-0.0336-0.1268-0.125-0.3241-0.43770.3695-0.07790.5677-0.01730.05730.60610.02070.511824.853630.8236141.804
112.22460.229-0.87591.8326-0.22043.49150.12350.05740.19770.02020.01220.0236-0.30490.0231-0.13170.40510.06790.03920.33080.00950.362722.307341.9137177.4523
121.3368-0.34520.51340.2881-0.26450.910.2026-0.0165-0.2075-0.0338-0.1110.14710.0863-0.118-0.05440.42280.02860.01450.3012-0.01540.402629.626112.6193192.9805
131.45540.1841-0.63560.8059-0.52230.99270.0850.0259-0.1682-0.2659-0.10750.1799-0.1712-0.1974-0.06370.4720.10950.03220.4055-0.02660.427914.928622.2363188.2403
141.2699-0.9119-0.18912.4405-0.14640.81740.03270.01560.02290.16120.06290.2111-0.0053-0.1561-0.06230.39690.04510.04580.3422-0.0070.383114.09920.4523189.6095
150.80420.15160.45881.874-0.61430.7136-0.0155-0.137-0.1507-0.0867-0.0538-0.1950.0070.06040.04850.58290.05140.11780.4113-0.02090.453822.96418.135195.9122
162.70081.0118-0.39461.992-0.44892.88020.1992-0.12690.14770.0895-0.1036-0.0557-0.2151-0.0155-0.0840.3680.00360.01660.2671-0.02290.306456.4918.2173196.2586
171.6215-1.0032-0.82670.44320.117-0.13820.33630.7977-0.1438-0.2519-0.3563-0.0220.0612-0.14070.05310.56070.04540.020.5782-0.02620.436743.679527.8802166.6757
181.6980.76680.55841.0482-0.30761.4786-0.1710.2705-0.0644-0.10090.18830.01090.18380.3336-0.01010.41370.05790.05230.5094-0.02060.441758.743820.7982172.8169
191.12730.36611.18870.4357-1.17152.49670.06480.3496-0.0538-0.1826-0.0169-0.03030.22980.182-0.02390.4580.06290.07020.4857-0.05990.419658.98421.5295170.5324
200.46940.61390.68810.4757-0.02641.07970.08240.60540.12450.1053-0.0940.172-0.2916-0.7395-0.01490.58130.06540.07610.71070.02040.496652.603130.6944168.6849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 136:282)A136 - 282
2X-RAY DIFFRACTION2(chain A and resid 283:336)A283 - 336
3X-RAY DIFFRACTION3(chain A and resid 337:365)A337 - 365
4X-RAY DIFFRACTION4(chain A and resid 366:445)A366 - 445
5X-RAY DIFFRACTION5(chain A and resid 446:477)A446 - 477
6X-RAY DIFFRACTION6(chain B and resid 136:282)B136 - 282
7X-RAY DIFFRACTION7(chain B and resid 283:336)B283 - 336
8X-RAY DIFFRACTION8(chain B and resid 337:365)B337 - 365
9X-RAY DIFFRACTION9(chain B and resid 366:445)B366 - 445
10X-RAY DIFFRACTION10(chain B and resid 446:477)B446 - 477
11X-RAY DIFFRACTION11(chain C and resid 136:282)C136 - 282
12X-RAY DIFFRACTION12(chain C and resid 283:336)C283 - 336
13X-RAY DIFFRACTION13(chain C and resid 337:365)C337 - 365
14X-RAY DIFFRACTION14(chain C and resid 366:445)C366 - 445
15X-RAY DIFFRACTION15(chain C and resid 446:478)C446 - 478
16X-RAY DIFFRACTION16(chain D and resid 136:282)D136 - 282
17X-RAY DIFFRACTION17(chain D and resid 283:336)D283 - 336
18X-RAY DIFFRACTION18(chain D and resid 337:365)D337 - 365
19X-RAY DIFFRACTION19(chain D and resid 366:445)D366 - 445
20X-RAY DIFFRACTION20(chain D and resid 446:476)D446 - 476

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