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- PDB-7pv6: CARM1 in complex with EML734 -

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Basic information

Entry
Database: PDB / ID: 7pv6
TitleCARM1 in complex with EML734
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-LRZ / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMarechal, N. / Cura, V. / Troffer-Charlier, N. / Bonnefond, L. / 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
DepositionOct 1, 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)170,01021
Polymers166,6374
Non-polymers3,37317
Water2,972165
1
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
hetero molecules

A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,18926
Polymers166,6374
Non-polymers3,55222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
2
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules

C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,83216
Polymers166,6374
Non-polymers3,19512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)75.000, 99.519, 208.460
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: 41659.246 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-LRZ / methyl 6-[3-[[~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]carbamimidoyl]amino]propylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate


Mass: 608.606 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H32N10O7 / 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: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20 mM Tris pH 7.5, 50 mM NaCl, 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.967 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.4→48.4 Å / Num. obs: 61974 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 50.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.053 / Rrim(I) all: 0.14 / Net I/σ(I): 11.3
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 7 % / Rmerge(I) obs: 2.017 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4383 / CC1/2: 0.547 / Rpim(I) all: 0.813 / Rrim(I) all: 2.177 / % possible all: 96.8

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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: 2.4→46.17 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 3083 4.99 %
Rwork0.191 58737 -
obs0.1934 61820 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.5 Å2 / Biso mean: 61.633 Å2 / Biso min: 26.61 Å2
Refinement stepCycle: final / Resolution: 2.4→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11282 0 455 165 11902
Biso mean--76.86 49.58 -
Num. residues----1410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.430.35851410.33542495263695
2.43-2.470.30441460.308926132759100
2.47-2.520.34231210.298726672788100
2.52-2.560.35811380.288426492787100
2.56-2.610.29821460.275826442790100
2.61-2.660.351390.272826292768100
2.66-2.720.2761380.249826442782100
2.72-2.790.29431280.230426912819100
2.79-2.860.27391440.227726532797100
2.86-2.930.28691290.221626412770100
2.93-3.020.31561340.233426782812100
3.02-3.120.30911460.24526532799100
3.12-3.230.29051380.230626482786100
3.23-3.360.27041340.205526732807100
3.36-3.510.23361250.187326792804100
3.51-3.690.24521350.17932685282099
3.69-3.930.21211590.17372638279799
3.93-4.230.18751450.141526782823100
4.23-4.650.16651470.133127192866100
4.65-5.330.21871330.133327482881100
5.33-6.710.22031500.183427542904100
6.71-46.170.18651670.16952858302599
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)
11.6435-0.7156-1.18821.27880.3792.35440.1091-0.07680.18130.0589-0.05660.0486-0.23910.0343-0.04820.4212-0.14160.02510.3971-0.01440.381855.168639.7419134.7418
21.138-0.04840.5712-0.40850.25630.9880.1662-0.0012-0.14450.0428-0.0536-0.0539-0.0450.1732-0.05440.2176-0.01780.02530.29520.00090.352746.274711.8765118.2101
30.28270.2406-0.06111.70110.79640.976-0.07420.05840.0206-0.03020.071-0.1104-0.12740.26050.01360.2818-0.0680.03270.53140.02580.414461.754220.2844123.0039
40.2290.2412-0.48371.8499-0.25721.5307-0.003-0.0869-0.0767-0.027-0.0204-0.1677-0.01990.30470.01490.2084-0.05020.00080.43730.01180.377162.142418.4323121.3949
5-0.09990.01710.20912.4681-0.34390.28730.0407-0.05480.00780.25480.0170.18380.0328-0.0114-0.05420.3221-0.04580.04260.48460.0240.379756.15719.8133121.9842
61.7059-0.1816-0.31741.67480.10142.21180.15010.1650.164-0.0269-0.00160.0527-0.2791-0.0591-0.1270.28430.07730.04880.30760.03440.337419.824119.7302114.9501
70.93220.5852-0.23950.54730.0783-0.02020.2238-0.156-0.01450.2569-0.13460.0691-0.1920.0585-0.04880.4243-0.03120.07940.4881-0.01690.355432.965726.6415144.775
81.9409-0.38781.05091.35430.36471.99540.1476-0.28480.1160.1120.00340.04420.0208-0.0669-0.18020.3464-0.01380.08450.47870.00740.42817.211621.2785138.3237
90.44970.0380.55040.82990.46471.8990.0796-0.17420.00560.1019-0.0777-0.0373-0.187-0.14190.00130.3215-0.03270.0590.4947-0.00850.350617.165721.9864140.7504
100.3398-0.35530.61990.86890.29311.59410.065-0.0017-0.0358-0.0619-0.0458-0.3124-0.28750.2842-0.02070.4615-0.13430.08880.588-0.03490.563824.732629.6149142.6673
111.9537-0.0387-0.71941.0697-0.2512.33050.0728-0.0350.19980.15150.05230.0207-0.32130.0761-0.10620.63910.01870.0730.3881-0.03490.411222.436940.9748178.0657
121.689-0.34090.6813-0.1739-0.18910.99010.1868-0.1548-0.0339-0.0279-0.0690.04470.0374-0.1898-0.08640.43430.00450.03710.26540.00050.37129.657612.4828194.7957
130.5962-0.24-0.47681.2921-0.51140.9064-0.00010.0397-0.04870.03270.06090.1718-0.1946-0.1115-0.06150.53090.02930.06020.44110.00460.460114.804322.0576189.8593
141.0197-0.6681-0.34981.7240.15281.11350.0118-0.0148-0.03360.22720.03260.22270.0012-0.1045-0.03330.4753-0.02190.05720.3748-0.02960.407214.143720.2101191.3695
150.61610.55940.2931.8289-0.22990.33380.04650.0481-0.0686-0.0770.07350.03950.0566-0.0377-0.1080.6350.05050.05490.5401-0.01350.468319.755911.3057190.9109
161.36130.5594-0.67621.5431-0.6491.47290.0404-0.06380.03140.1524-0.0494-0.0855-0.20020.06180.00130.5315-0.0673-0.02150.312-0.01850.389656.697418.2374198.0056
170.9787-0.7460.06640.5338-0.29980.15410.11350.4657-0.1302-0.0329-0.16010.0472-0.00890.11180.03040.5747-0.02750.04740.5495-0.03170.453643.853826.3552168.0869
181.8050.19860.05030.84430.06871.72030.05030.41960.0822-0.0272-0.12110.03420.2488-0.05310.07820.542-0.00180.09780.5009-0.00440.516359.022219.7304174.5203
191.29180.04350.52630.7302-0.84751.4273-0.04510.3014-0.1348-0.0607-0.0686-0.07310.0580.09950.08480.45520.0110.04150.5004-0.05160.428859.172720.3513172.085
200.94190.06870.76391.11370.14650.87560.14740.10390.08720.3331-0.0940.2156-0.1684-0.2595-0.03020.63020.01230.06780.56-0.00140.525752.217728.5208170.3726
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 446:497)A446 - 497
6X-RAY DIFFRACTION6(chain B and resid 135:282)B135 - 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 446:497)C446 - 497
16X-RAY DIFFRACTION16(chain D and resid 135:282)D135 - 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 446:477)D446 - 477

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