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- PDB-5lgq: Crystal structure of mouse CARM1 in complex with ligand P2C3s -

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Basic information

Entry
Database: PDB / ID: 5lgq
TitleCrystal structure of mouse CARM1 in complex with ligand P2C3s
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 / mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / translation activator activity / CRD-mediated mRNA stabilization / histone H3R2 methyltransferase activity ...histone H3R26 methyltransferase activity / mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / translation activator activity / CRD-mediated mRNA stabilization / 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 / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Estrogen-dependent gene expression / Deadenylation of mRNA / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / positive regulation of cytoplasmic translation / mRNA stabilization / regulatory ncRNA-mediated gene silencing / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation / histone methyltransferase activity / cell leading edge / nuclear replication fork / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of fat cell differentiation / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / nuclear receptor-mediated steroid hormone signaling pathway / response to cAMP / protein localization to chromatin / estrogen receptor signaling pathway / catalytic step 2 spliceosome / nuclear receptor coactivator activity / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / lysine-acetylated histone binding / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / RNA polymerase II transcription regulator complex / lamellipodium / methylation / cell population proliferation / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / 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 / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / Poly-adenylate binding protein, unique 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 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / Poly-adenylate binding protein, unique 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 / Arginine methyltransferase oligomerization subdomain / 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 / Distorted Sandwich / RNA-binding domain superfamily / 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
Chem-8ZB / 1,2-DIMETHOXYETHANE / DI(HYDROXYETHYL)ETHER / Chem-PG6 / 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 / Resolution: 2.11 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: Non-polymer description
Revision 1.2Apr 12, 2017Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
F: Polyadenylate-binding protein 1
E: Polyadenylate-binding protein 1
G: Polyadenylate-binding protein 1
H: Polyadenylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,52026
Polymers168,0918
Non-polymers2,42918
Water15,115839
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19490 Å2
ΔGint-72 kcal/mol
Surface area50930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.706, 99.011, 207.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-838-

HOH

21C-791-

HOH

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Components

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

#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: 1172.375 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P11940

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Non-polymers , 7 types, 857 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Chemical ChemComp-DXE / 1,2-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


Mass: 266.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H26O6
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-8ZB / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-propyl-oxolane-3,4-diol


Mass: 279.295 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H17N5O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 839 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris-HCl pH 8.5 14% PEG 3350 200 mM A.S.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.073 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.073 Å / Relative weight: 1
ReflectionResolution: 2.11→48.152 Å / Num. obs: 89266 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 32.74 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9
Reflection shellResolution: 2.11→2.15 Å / Redundancy: 4.7 % / Rmerge(I) obs: 2.021 / Mean I/σ(I) obs: 0.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2386: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3


Resolution: 2.11→48.152 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 4423 4.96 %Random selection
Rwork0.1866 ---
obs0.189 89162 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→48.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11346 0 85 839 12270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211841
X-RAY DIFFRACTIONf_angle_d0.5316040
X-RAY DIFFRACTIONf_dihedral_angle_d16.9927035
X-RAY DIFFRACTIONf_chiral_restr0.0431737
X-RAY DIFFRACTIONf_plane_restr0.0032105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.1340.34021340.35592810X-RAY DIFFRACTION100
2.134-2.15910.39631510.33082751X-RAY DIFFRACTION100
2.1591-2.18540.3391490.32882794X-RAY DIFFRACTION100
2.1854-2.21310.35531550.30742792X-RAY DIFFRACTION100
2.2131-2.24220.35121530.29382764X-RAY DIFFRACTION100
2.2422-2.27290.3451490.30282774X-RAY DIFFRACTION100
2.2729-2.30540.32391420.2752805X-RAY DIFFRACTION100
2.3054-2.33980.35091450.26972824X-RAY DIFFRACTION100
2.3398-2.37640.33091260.25072783X-RAY DIFFRACTION100
2.3764-2.41530.28961460.24212821X-RAY DIFFRACTION100
2.4153-2.4570.2561610.23742741X-RAY DIFFRACTION100
2.457-2.50160.28151330.22872832X-RAY DIFFRACTION100
2.5016-2.54980.30131390.22462819X-RAY DIFFRACTION100
2.5498-2.60180.26711520.22172787X-RAY DIFFRACTION100
2.6018-2.65840.25961470.21082812X-RAY DIFFRACTION100
2.6584-2.72020.29681500.2192795X-RAY DIFFRACTION100
2.7202-2.78820.31031330.21592824X-RAY DIFFRACTION100
2.7882-2.86360.25081420.20462829X-RAY DIFFRACTION100
2.8636-2.94780.26271400.19632827X-RAY DIFFRACTION100
2.9478-3.0430.22751440.18892809X-RAY DIFFRACTION100
3.043-3.15170.25741680.19362811X-RAY DIFFRACTION100
3.1517-3.27790.21661480.18392840X-RAY DIFFRACTION100
3.2779-3.4270.21771320.17882842X-RAY DIFFRACTION100
3.427-3.60770.22621330.15592846X-RAY DIFFRACTION100
3.6077-3.83360.19151610.1382841X-RAY DIFFRACTION100
3.8336-4.12940.17051620.12652858X-RAY DIFFRACTION100
4.1294-4.54470.13611540.11472849X-RAY DIFFRACTION100
4.5447-5.20170.18781340.11452919X-RAY DIFFRACTION100
5.2017-6.5510.20481630.15912912X-RAY DIFFRACTION100
6.551-48.16410.22311770.18113028X-RAY DIFFRACTION99
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)
11.1897-0.1691-0.17050.57860.07180.5104-0.0597-0.1710.11660.13620.00390.029-0.15120.062500.2932-0.0280.02340.2048-0.05140.280154.737440.0357133.553
20.37570.1680.02110.02430.03070.30020.00650.0284-0.0591-0.03860.03060.0094-0.04930.08660.01230.15230.0030.00860.113-0.00970.297547.859911.9811119.3793
30.2427-0.0290.0011.0356-0.22270.3079-0.0357-0.0375-0.0496-0.18130.0404-0.03-0.02730.1254-0.00040.1851-0.02510.04710.1883-0.01430.281860.034219.4684119.3546
40.7771-0.4106-0.17440.70610.2980.93780.07290.01-0.00080.00420.0250.0045-0.216-0.15210.15030.18910.07720.01190.16620.03780.261519.148519.8653114.9702
50.29680.13060.08990.03020.04710.13820.1762-0.1927-0.1380.2033-0.0223-0.01740.06820.1088-00.4008-0.0190.06220.3523-0.01810.283438.170128.6837148.4847
60.24980.036-0.06210.2960.31150.35620.1457-0.1310.1121-0.0672-0.1322-0.04950.1762-0.178500.37360.01310.05490.36420.03670.340916.984421.677137.6019
70.2828-0.0853-0.25480.03560.12230.36160.0717-0.1978-0.02510.0563-0.02250.0401-0.0724-0.123100.30740.01360.02910.31340.03460.279916.902522.4894140.0853
80.1801-0.05940.15110.16340.03430.1670.1284-0.1664-0.0337-0.0272-0.0313-0.1275-0.09610.0575-00.429-0.0010.07350.40360.00270.408424.807429.2504141.5051
90.7448-0.1238-0.48460.2658-0.23230.7108-0.02820.0540.12370.04210.0404-0.001-0.2-0.124800.45440.05440.01780.44990.01170.337423.160841.7521175.38
100.2961-0.04520.20160.0062-0.01030.37180.0639-0.068-0.07860.0033-0.0432-0.0025-0.0237-0.1906-0.0020.33860.03360.03410.4079-0.01560.2725.971721.1027191.103
110.3306-0.0458-0.36870.7042-0.13430.4454-0.06560.0577-0.07690.09050.01840.0987-0.0972-0.117600.37470.04710.06670.4357-0.02730.304616.23720.1796191.1103
120.79640.2651-0.51830.6155-0.04380.52430.111-0.1024-0.02240.0804-0.1177-0.0996-0.10860.08200.3437-0.0749-0.00570.3912-0.01440.281757.161418.0997196.1389
130.264-0.2005-0.12470.13570.05070.35580.23750.106-0.0645-0.1295-0.10220.01010.0020.0276-00.458-0.00950.06860.5001-0.04960.307239.788427.4607164.0807
140.1657-0.06710.04670.1709-0.15930.14850.04460.2497-0.1365-0.0855-0.1696-0.0230.05130.2662-0.00010.4597-0.01070.04440.62150.00310.370563.429222.8891175.1794
150.14130.09060.02360.0943-0.05560.10710.09830.148-0.1197-0.0576-0.05610.00820.08370.177300.42990.06020.02450.4742-0.02550.299158.438917.2739170.5111
160.3374-0.24540.22310.206-0.10340.22310.22130.1626-0.01620.0365-0.22580.0564-0.1775-0.0453-0.00010.50150.01870.04960.60850.00480.352354.527129.1754169.2136
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 B and resid 135:293)
5X-RAY DIFFRACTION5(chain B and resid 294:336)
6X-RAY DIFFRACTION6(chain B and resid 337:365)
7X-RAY DIFFRACTION7(chain B and resid 366:445)
8X-RAY DIFFRACTION8(chain B and resid 446:477)
9X-RAY DIFFRACTION9(chain C and resid 136:257)
10X-RAY DIFFRACTION10(chain C and resid 258:336)
11X-RAY DIFFRACTION11(chain C and resid 337:478)
12X-RAY DIFFRACTION12(chain D and resid 136:293)
13X-RAY DIFFRACTION13(chain D and resid 294:344)
14X-RAY DIFFRACTION14(chain D and resid 345:372)
15X-RAY DIFFRACTION15(chain D and resid 373:430)
16X-RAY DIFFRACTION16(chain D and resid 431:477)

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