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- PDB-5lgr: Crystal structure of mouse CARM1 in complex with ligand P1C3u -

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Basic information

Entry
Database: PDB / ID: 5lgr
TitleCrystal structure of mouse CARM1 in complex with ligand P1C3u
Components
  • Histone-arginine methyltransferase CARM1
  • Polyadenylate-binding protein 1
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 / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / endochondral bone morphogenesis / CRD-mediated mRNA stabilization / histone H3R2 methyltransferase activity ...histone H3R26 methyltransferase activity / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / endochondral bone morphogenesis / CRD-mediated mRNA stabilization / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / negative regulation of dendrite development / type I protein arginine methyltransferase / Cytoprotection by HMOX1 / protein-arginine omega-N asymmetric methyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / protein methyltransferase activity / Estrogen-dependent gene expression / Deadenylation of mRNA / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / positive regulation of cytoplasmic translation / protein-arginine N-methyltransferase activity / mRNA stabilization / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of epithelial cell apoptotic process / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Translation initiation complex formation / : / positive regulation of transcription by RNA polymerase I / histone methyltransferase activity / nuclear replication fork / cell leading edge / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of fat cell differentiation / intracellular estrogen receptor signaling pathway / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / intracellular steroid hormone receptor signaling pathway / response to cAMP / protein localization to chromatin / catalytic step 2 spliceosome / nuclear receptor coactivator activity / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / lysine-acetylated histone binding / cytoplasmic ribonucleoprotein granule / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / cytoplasmic stress granule / RNA polymerase II transcription regulator complex / lamellipodium / methylation / DNA-binding transcription factor binding / cell population proliferation / transcription coactivator activity / transcription cis-regulatory region binding / ribonucleoprotein complex / focal adhesion / mRNA binding / 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 / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal ...: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / 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 / RNA recognition motif domain, eukaryote / RNA recognition motif / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Distorted Sandwich / PH-like domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / 1,2-DIMETHOXYETHANE / L-PROLINAMIDE / DI(HYDROXYETHYL)ETHER / Chem-PG6 / Chem-QVR / Polyadenylate-binding protein 1 / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMarechal, N. / Troffer-Charlier, N. / Cura, V. / Bonnefond, L. / Cavarelli, J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Transition state mimics are valuable mechanistic probes for structural studies with the arginine methyltransferase CARM1.
Authors: van Haren, M.J. / Marechal, N. / Troffer-Charlier, N. / Cianciulli, A. / Sbardella, G. / Cavarelli, J. / Martin, N.I.
History
DepositionJul 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Jan 10, 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: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
E: Polyadenylate-binding protein 1
F: Polyadenylate-binding protein 1
G: Polyadenylate-binding protein 1
H: Polyadenylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,08128
Polymers168,4968
Non-polymers2,58520
Water13,781765
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22620 Å2
ΔGint-102 kcal/mol
Surface area49610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.831, 98.544, 208.336
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#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 frugiperda (fall armyworm)
References: UniProt: Q9WVG6, type I protein arginine methyltransferase
#2: Protein/peptide
Polyadenylate-binding protein 1 / Poly(A)-binding protein 1


Mass: 1273.483 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: PABP1(447-459) / Source: (synth.) Homo sapiens (human) / References: UniProt: P11940

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Non-polymers , 9 types, 785 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DXE / 1,2-DIMETHOXYETHANE / Dimethoxyethane


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-QVR / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol


Mass: 277.279 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H15N5O3 / Details: PABP1(447-459)
#9: Chemical
ChemComp-LPD / L-PROLINAMIDE


Type: L-peptide linking / Mass: 114.146 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10N2O / Details: PABP1(447-459)
#10: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O / Details: PABP1(447-459)
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 765 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl pH 8.5 100 mM PEG 3350 14 % Ammonium Sulfate 200 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→47.95 Å / Num. obs: 104813 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 29.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.073 / Rrim(I) all: 0.189 / Net I/σ(I): 8 / Num. measured all: 700081
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.036.63.226199.9
10.95-47.955.60.033198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.25data scaling
PHENIXdev_2386refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3


Resolution: 2→46.048 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.32
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 5213 4.98 %Random Selection
Rwork0.192 ---
obs0.1941 104667 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.74 Å2 / Biso mean: 42.9158 Å2 / Biso min: 14.24 Å2
Refinement stepCycle: final / Resolution: 2→46.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11457 0 142 765 12364
Biso mean--65.89 39.77 -
Num. residues----1423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211842
X-RAY DIFFRACTIONf_angle_d0.5416034
X-RAY DIFFRACTIONf_chiral_restr0.0571742
X-RAY DIFFRACTIONf_plane_restr0.0022105
X-RAY DIFFRACTIONf_dihedral_angle_d15.0556985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02270.38861880.362333043492100
2.0227-2.04650.38751810.348632143395100
2.0465-2.07150.36511940.339232653459100
2.0715-2.09770.38761450.323433233468100
2.0977-2.12530.30491590.303332703429100
2.1253-2.15440.32441700.294732763446100
2.1544-2.18520.34671770.294332743451100
2.1852-2.21780.34371850.282132833468100
2.2178-2.25250.30641780.266432733451100
2.2525-2.28940.3141830.256233013484100
2.2894-2.32890.32731570.261332843441100
2.3289-2.37120.30121540.245332723426100
2.3712-2.41680.24921700.229133263496100
2.4168-2.46620.25521830.215832633446100
2.4662-2.51980.28971510.222333253476100
2.5198-2.57840.24981830.213632903473100
2.5784-2.64290.30191650.219332953460100
2.6429-2.71430.24051760.206332753451100
2.7143-2.79420.23461680.190733083476100
2.7942-2.88440.23681720.189533383510100
2.8844-2.98740.23571550.188833523507100
2.9874-3.1070.24251890.192332693458100
3.107-3.24840.23931670.199333433510100
3.2484-3.41960.20351710.173333183489100
3.4196-3.63380.2061660.156833423508100
3.6338-3.91420.17891900.141933453535100
3.9142-4.30780.1541820.123433633545100
4.3078-4.93060.17411670.116434073574100
4.9306-6.20960.18751800.148534263606100
6.2096-46.06010.20682070.1793530373799
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)
10.6311-0.0424-0.1340.52920.04720.4118-0.008-0.18660.12230.0773-0.0316-0.006-0.0718-0.021-0.04290.2446-0.01960.00820.1519-0.06980.239755.022340.0381134.6185
20.32480.06880.0931-0.0009-0.00130.23290.0769-0.0883-0.0240.0234-0.02840.0866-0.03980.09370.03430.1518-0.01520.00530.0236-0.01770.325647.913311.876119.8425
30.11020.0607-0.00230.6112-0.05470.8227-0.0314-0.0381-0.0308-0.07680.0119-0.0492-0.01020.1107-0.00410.1858-0.02410.03480.1347-0.02280.265360.369419.334120.0025
40.40530.0028-0.18660.47910.21380.63120.08830.0189-0.0367-0.0250.00130.0062-0.1739-0.14630.08590.2160.05660.01190.13380.01450.237718.986419.8538115.5253
50.09420.127-0.06790.0738-0.09080.07110.0772-0.1457-0.07090.07520.0123-0.0004-0.02990.020700.364-0.02760.02910.3924-0.02440.278738.139528.8109149.1455
60.25430.23070.09750.2260.17460.24140.023-0.09480.02220.162-0.07780.054-0.066-0.035500.33680.02820.06410.32380.01830.312517.014721.706138.1959
70.6132-0.0104-0.14240.18760.14020.53270.0602-0.2613-0.05230.04870.0053-0.0259-0.1067-0.19620.00770.24030.00560.01680.23370.01340.225916.928622.3773140.6834
80.21170.09940.21720.24810.05430.1930.042-0.29590.070.03660.0295-0.13020.03310.149800.31990.02510.02110.27340.01280.270424.522630.101142.2515
90.62320.0711-0.19660.4079-0.43360.4919-0.0999-0.06430.1045-0.01010.06790.0227-0.162-0.1616-00.41630.04750.01630.5533-0.03030.309823.216641.7263176.157
100.08530.06650.17670.06440.15530.27730.0777-0.0979-0.06980.005-0.030.0236-0.0652-0.1597-0.00350.25160.02840.0520.4462-0.01360.259626.056821.0349192.1097
110.3927-0.1233-0.32760.5894-0.07060.3493-0.0350.0398-0.03940.0714-0.00120.0608-0.076-0.1263-00.33150.04190.0570.569-0.03190.316416.32420.0846191.9802
120.33080.1097-0.01540.7649-0.21990.44960.1144-0.1166-0.03890.0182-0.1018-0.0919-0.11120.1374-00.3275-0.0860.0230.5615-0.04960.300957.295818.0942197.2059
130.1355-0.2302-0.08740.20890.19680.16330.02940.0639-0.0096-0.0042-0.007-0.0294-0.05080.008400.41510.01670.03650.5466-0.05110.296939.996527.6432165.0067
140.1045-0.032-0.05160.1912-0.21130.259-0.11090.0010.0107-0.1189-0.03650.0271-0.15770.3639-00.4227-0.04920.05640.611-0.040.344463.858123.2651176.9082
150.16020.0755-0.12760.0505-0.11130.22010.0570.0545-0.0358-0.05-0.0891-0.0592-0.07720.1643-00.39860.03750.02240.5857-0.04680.324358.565517.3603171.5471
160.1844-0.00650.12730.187-0.14920.15710.22470.04140.05730.0179-0.00960.0591-0.1366-0.056400.477-0.00610.02150.5945-0.04130.326654.142228.7901170.4588
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 283:349)A283 - 349
3X-RAY DIFFRACTION3(chain A and resid 350:478)A350 - 478
4X-RAY DIFFRACTION4(chain B and resid 135:293)B135 - 293
5X-RAY DIFFRACTION5(chain B and resid 294:336)B294 - 336
6X-RAY DIFFRACTION6(chain B and resid 337:365)B337 - 365
7X-RAY DIFFRACTION7(chain B and resid 366:445)B366 - 445
8X-RAY DIFFRACTION8(chain B and resid 446:477)B446 - 477
9X-RAY DIFFRACTION9(chain C and resid 136:257)C136 - 257
10X-RAY DIFFRACTION10(chain C and resid 258:336)C258 - 336
11X-RAY DIFFRACTION11(chain C and resid 337:478)C337 - 478
12X-RAY DIFFRACTION12(chain D and resid 136:293)D136 - 293
13X-RAY DIFFRACTION13(chain D and resid 294:344)D294 - 344
14X-RAY DIFFRACTION14(chain D and resid 345:372)D345 - 372
15X-RAY DIFFRACTION15(chain D and resid 373:430)D373 - 430
16X-RAY DIFFRACTION16(chain D and resid 431:477)D431 - 477

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