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- PDB-5lkj: Crystal structure of mouse CARM1 in complex with ligand SA684 -

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Basic information

Entry
Database: PDB / ID: 5lkj
TitleCrystal structure of mouse CARM1 in complex with ligand SA684
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE / PROTEIN ARGININE METHYLTRANSFERASE / CATALYTIC DOMAIN / CHROMATIN REGULATOR / MRNA PROCESSING / MRNA SPLICING / NUCLEUS / S-ADENOSYL-L-METHIONINE / TRANSCRIPTION / TRANSCRIPTION REGULATION
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) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich ...Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-6YB / 1,2-DIMETHOXYETHANE / DI(HYDROXYETHYL)ETHER / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.595 Å
AuthorsCura, V. / Marechal, N. / Mailliot, J. / Troffer-Charlier, N. / Hassenboehler, P. / Wurtz, J.M. / Bonnefond, L. / Cavarelli, J.
CitationJournal: To Be Published
Title: Crystal structure of mouse CARM1 in complex with ligands
Authors: Cura, V. / Marechal, N. / Mailliot, J. / Troffer-Charlier, N. / Hassenboehler, P. / Wurtz, J.M. / Bonnefond, L. / Cavarelli, J.
History
DepositionJul 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: 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)171,34425
Polymers167,9434
Non-polymers3,40221
Water2,414134
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13640 Å2
ΔGint-2 kcal/mol
Surface area53120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.637, 98.161, 206.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 41985.637 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 frugiperda (fall armyworm)
References: UniProt: Q9WVG6, type I protein arginine methyltransferase

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Non-polymers , 6 types, 155 molecules

#2: Chemical
ChemComp-6YB / (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-carbamimidamidoethyl)amino]-2-azanyl-butanoic acid


Mass: 452.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H28N10O5
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical
ChemComp-DXE / 1,2-DIMETHOXYETHANE


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM BTP pH 7.5 30% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.595→20 Å / Num. obs: 47431 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 58.3 Å2 / Rsym value: 0.084 / Net I/σ(I): 24.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3


Resolution: 2.595→19.902 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / Phase error: 21.97
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 2364 4.99 %Random selection
Rwork0.1889 ---
obs0.1905 47376 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.595→19.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11258 0 233 134 11625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411788
X-RAY DIFFRACTIONf_angle_d0.87615949
X-RAY DIFFRACTIONf_dihedral_angle_d18.064360
X-RAY DIFFRACTIONf_chiral_restr0.041735
X-RAY DIFFRACTIONf_plane_restr0.0042025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5954-2.64830.28151340.23272410X-RAY DIFFRACTION92
2.6483-2.70580.24171320.22882604X-RAY DIFFRACTION100
2.7058-2.76850.30191280.23222647X-RAY DIFFRACTION100
2.7685-2.83760.25771370.22452609X-RAY DIFFRACTION100
2.8376-2.91410.28811360.21892633X-RAY DIFFRACTION100
2.9141-2.99950.26851320.22672680X-RAY DIFFRACTION100
2.9995-3.0960.23771500.22582607X-RAY DIFFRACTION100
3.096-3.20620.23541370.21642621X-RAY DIFFRACTION100
3.2062-3.3340.21211360.20642655X-RAY DIFFRACTION100
3.334-3.4850.25161200.20062662X-RAY DIFFRACTION100
3.485-3.66770.22891330.1912648X-RAY DIFFRACTION100
3.6677-3.89590.20611590.17422660X-RAY DIFFRACTION100
3.8959-4.19410.20131410.15752662X-RAY DIFFRACTION100
4.1941-4.61140.16271420.1482684X-RAY DIFFRACTION100
4.6114-5.26780.17541330.15172712X-RAY DIFFRACTION100
5.2678-6.59650.22961490.20392728X-RAY DIFFRACTION100
6.5965-19.90280.21271650.18892790X-RAY DIFFRACTION98
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)
11.1179-0.4767-0.08071.05830.24590.88280.0306-0.06490.180.1409-0.12570.1552-0.14520.02740.00010.3767-0.10880.05850.3222-0.08440.374754.97840.0021133.1293
21.10290.4890.214-0.2262-0.02350.66470.23440.019-0.01210.0468-0.06610.01980.00370.08030.33560.1428-0.04450.03770.2113-0.01440.397547.831411.8009118.8407
30.67960.2767-0.10742.3175-0.15231.68510.00220.0375-0.031-0.075-0.0335-0.00390.0190.0422-0.09470.1482-0.07280.06770.3029-0.02260.33460.217719.0836118.8648
40.02750.0671-0.14580.1252-0.16870.08090.44780.3341-0.02640.25-0.1220.13680.20490.13030.00010.56280.0107-0.01490.4306-0.05850.551461.3732-3.817132.9914
51.0005-0.0749-0.55541.94690.35531.64440.2040.22360.1350.07130.02630.087-0.2569-0.20020.30770.21260.09350.09260.29030.06380.347118.920519.6533114.669
60.88660.43860.4999-0.4485-0.2262-0.12170.3729-0.4588-0.22080.6489-0.13190.1996-0.20190.020.05710.4712-0.07770.12920.4856-0.04150.440338.353128.7613148.1975
70.6161-0.0160.13890.73550.92921.00340.0943-0.24520.25490.0231-0.0093-0.1444-0.1725-0.31450.03960.32170.03370.17250.45440.0380.570717.20521.5666137.5383
80.7786-0.1331-0.1071-0.0136-0.10341.36460.0831-0.11320.00550.13690.02590.0971-0.2292-0.08910.00020.31280.04790.09570.31160.00620.398716.927622.2474140.0513
90.43080.02220.40330.7290.22390.33680.0956-0.0447-0.0112-0.03230.045-0.5682-0.46590.0757-0.01330.49830.0310.20090.5226-0.00370.604824.940329.3048141.3958
100.64720.3699-0.75210.3784-0.62351.3933-0.04160.12010.03220.19990.15710.0815-0.36840.0013-0.00010.80490.09590.08630.52480.02390.474323.056442.0043174.7438
110.5284-0.0497-0.06410.4236-0.27930.45190.1157-0.0779-0.32590.26660.0660.2499-0.2082-0.1370.12970.67670.06970.10150.3543-0.01320.262725.991821.0501190.4213
120.2593-0.1612-0.24811.25850.15780.7652-0.06890.0303-0.05260.21790.05730.15760.0029-0.1239-00.6960.14060.18720.58220.00840.451816.153619.9999190.4804
130.0549-0.0115-0.09670.05610.09210.09780.1544-0.04880.0379-0.0699-0.0106-0.13480.0704-0.183100.93080.0761-0.0540.8188-0.02910.676213.3285-2.0584176.8595
140.19160.3246-0.29561.515-0.6680.84940.1955-0.1157-0.00880.1903-0.2594-0.1031-0.33670.19890.00010.788-0.191-0.03050.56420.01440.380357.18418.1171195.3429
150.4991-0.4970.0567-0.03280.03250.28820.01190.335-0.1588-0.20260.0343-0.0698-0.19910.02070.00040.7337-0.02550.09490.5872-0.02240.446539.69227.7339163.1408
160.27370.06080.11820.2433-0.30380.3964-0.19870.2651-0.22580.2697-0.15220.3865-0.33270.79970.00020.7361-0.11950.04940.7383-0.00930.545463.528623.0638174.8178
170.47360.4521-0.16160.4163-0.40940.25670.09920.127-0.10490.0743-0.14140.0934-0.1370.2285-00.6007-0.05690.06870.5611-0.03210.391858.264617.2281169.5312
180.29190.17330.52410.29110.14940.45860.14260.1035-0.29670.0981-0.20410.36-0.590.05240.00080.7763-0.01240.10370.6306-0.0080.497253.972928.8129168.4142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 136:282)
2X-RAY DIFFRACTION2(chain A and resid 283:349)
3X-RAY DIFFRACTION3(chain A and resid 350:478)
4X-RAY DIFFRACTION4(chain A and resid 479:496)
5X-RAY DIFFRACTION5(chain B and resid 136:293)
6X-RAY DIFFRACTION6(chain B and resid 294:336)
7X-RAY DIFFRACTION7(chain B and resid 337:365)
8X-RAY DIFFRACTION8(chain B and resid 366:445)
9X-RAY DIFFRACTION9(chain B and resid 446:478)
10X-RAY DIFFRACTION10(chain C and resid 136:257)
11X-RAY DIFFRACTION11(chain C and resid 258:336)
12X-RAY DIFFRACTION12(chain C and resid 337:478)
13X-RAY DIFFRACTION13(chain C and resid 479:496)
14X-RAY DIFFRACTION14(chain D and resid 136:293)
15X-RAY DIFFRACTION15(chain D and resid 294:344)
16X-RAY DIFFRACTION16(chain D and resid 345:372)
17X-RAY DIFFRACTION17(chain D and resid 373:430)
18X-RAY DIFFRACTION18(chain D and resid 431:478)

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