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- PDB-5lgp: Crystal structure of mouse CARM1 in complex with ligand P1C3s -

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Basic information

Entry
Database: PDB / ID: 5lgp
TitleCrystal structure of mouse CARM1 in complex with ligand P1C3s
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
Chem-8ZB / L-PROLINAMIDE / 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: 2.04 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 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 / diffrn_radiation_wavelength / 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)170,48421
Polymers168,6008
Non-polymers1,88413
Water13,601755
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22160 Å2
ΔGint-108 kcal/mol
Surface area48240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.794, 98.714, 207.253
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
11D-728-

HOH

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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: 1299.521 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: URG is a modified ARG residue ARP is an acetylated PRO residue
Source: (synth.) Homo sapiens (human) / References: UniProt: P11940

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Non-polymers , 4 types, 768 molecules

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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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
Details: URG is a modified ARG residue ARP is an acetylated PRO residue
#5: Chemical
ChemComp-LPD / L-PROLINAMIDE


Type: L-peptide linking / Mass: 114.146 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10N2O
Details: URG is a modified ARG residue ARP is an acetylated PRO residue
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 755 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris-HCl pH 8.5 16% PEG 3350 200 mM A.S.

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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: 2.04→48 Å / Num. obs: 98498 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 31.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Net I/σ(I): 9.7
Reflection shellResolution: 2.04→2.07 Å / Redundancy: 6.4 % / Rmerge(I) obs: 2.331 / Mean I/σ(I) obs: 0.8 / CC1/2: 0.313 / % possible all: 100

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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: 2.04→48 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.65
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 4879 4.96 %Random selection
Rwork0.1873 ---
obs0.1889 98404 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.04→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11449 0 20 755 12224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611766
X-RAY DIFFRACTIONf_angle_d0.69115944
X-RAY DIFFRACTIONf_dihedral_angle_d12.8976959
X-RAY DIFFRACTIONf_chiral_restr0.0481739
X-RAY DIFFRACTIONf_plane_restr0.0042094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.06320.33821850.33183075X-RAY DIFFRACTION100
2.0632-2.08750.31651370.31293084X-RAY DIFFRACTION100
2.0875-2.11290.31561500.29283107X-RAY DIFFRACTION100
2.1129-2.13970.33381520.28693130X-RAY DIFFRACTION100
2.1397-2.16780.31721690.2853019X-RAY DIFFRACTION100
2.1678-2.19750.29451670.28343094X-RAY DIFFRACTION100
2.1975-2.22890.3171830.27093046X-RAY DIFFRACTION100
2.2289-2.26220.29981580.25853107X-RAY DIFFRACTION100
2.2622-2.29750.26651650.25083077X-RAY DIFFRACTION100
2.2975-2.33520.2631540.23613089X-RAY DIFFRACTION100
2.3352-2.37550.27651410.23793086X-RAY DIFFRACTION100
2.3755-2.41860.28481690.22473104X-RAY DIFFRACTION100
2.4186-2.46520.20941640.21513092X-RAY DIFFRACTION100
2.4652-2.51550.25661480.21573083X-RAY DIFFRACTION100
2.5155-2.57020.23881640.20143099X-RAY DIFFRACTION100
2.5702-2.630.23911580.20193102X-RAY DIFFRACTION100
2.63-2.69570.2561720.20063107X-RAY DIFFRACTION100
2.6957-2.76860.24441400.19913126X-RAY DIFFRACTION100
2.7686-2.85010.22091670.19813075X-RAY DIFFRACTION100
2.8501-2.9420.23031500.18933145X-RAY DIFFRACTION100
2.942-3.04720.21951650.18643100X-RAY DIFFRACTION100
3.0472-3.16920.22651740.19383098X-RAY DIFFRACTION100
3.1692-3.31340.21551610.18023140X-RAY DIFFRACTION100
3.3134-3.4880.19681440.17073137X-RAY DIFFRACTION100
3.488-3.70650.20851680.15243158X-RAY DIFFRACTION100
3.7065-3.99250.16211780.14463141X-RAY DIFFRACTION100
3.9925-4.3940.15731750.13013159X-RAY DIFFRACTION100
4.394-5.02930.15391480.12673195X-RAY DIFFRACTION100
5.0293-6.33410.21721770.15873207X-RAY DIFFRACTION100
6.3341-48.02750.19541960.18253343X-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)
11.6096-0.32240.04211.23660.05971.7988-0.0091-0.18680.26290.1108-0.05520.0461-0.28660.03720.05870.3051-0.03430.03250.22-0.06260.317354.971340.0985133.7905
21.75970.64320.69170.12830.22290.59480.0841-0.0696-0.09870.059-0.03590.06550.00720.0207-0.04360.23110.00150.01150.1488-0.0180.321447.861511.9278119.2948
30.4197-0.04140.0141.8125-0.02441.5196-0.0148-0.0191-0.0522-0.20050.0113-0.09410.05860.13550.00020.2182-0.03510.05160.2273-0.01060.320960.305919.4203119.3978
41.1420.0024-0.2541.08540.58891.81460.0850.04010.0539-0.0936-0.0250.0377-0.2069-0.1463-0.07080.240.06080.01430.17290.03650.291418.971719.7937114.9256
53.07521.4777-0.55930.6968-0.37930.25520.295-0.41550.08990.2723-0.14110.053-0.07940.0775-0.13310.379-0.01410.03530.3824-0.01520.289238.098128.8555148.4087
62.48920.36750.51490.76180.51861.82860.0655-0.25290.03330.0734-0.0990.13850.0741-0.22330.02390.28610.00160.05030.29090.00330.323117.02121.7172137.5239
71.05940.1025-0.29310.8529-0.56792.57750.1222-0.17570.1111-0.01720.0168-0.1605-0.17780.1422-0.15260.2991-0.02690.03190.2432-0.01860.323924.472830.1291141.5206
81.91950.0478-0.01671.427-0.36471.521-0.05850.02250.2068-0.03760.0480.0132-0.2527-0.16720.00730.42890.04710.02940.4346-0.00070.315723.205241.8111175.2808
90.47880.07630.25370.09850.05950.57470.1134-0.0679-0.0478-0.0793-0.05320.1061-0.0799-0.15-0.0730.29920.01220.03270.4196-0.01260.283326.062921.0705191.0909
100.8012-0.0647-0.07181.63-0.60860.926-0.0420.0228-0.08920.12810.05110.1636-0.0093-0.1951-0.01320.29870.04140.06660.4816-0.03250.288716.215220.161191.065
111.10250.1069-0.64081.533-0.35881.43140.0865-0.1636-0.01240.1016-0.0864-0.1933-0.13160.1925-0.0080.2917-0.0789-0.00580.4444-0.04250.293357.27218.0544196.2038
122.0039-1.3556-0.14590.92510.20470.18610.18580.38530.0485-0.2237-0.1466-0.07460.0391-0.0056-0.05350.419-0.02050.05470.5037-0.02630.295239.972227.7197164.1251
131.5501-0.17770.20731.24880.34142.4987-0.06440.1877-0.1235-0.06690.0859-0.17540.05860.709-0.03830.35890.00380.04270.5742-0.01060.34563.779623.1656175.9871
140.2830.21660.0610.7584-0.47841.75540.03010.1154-0.0621-0.1539-0.0478-0.1459-0.00510.27350.0470.344-0.00210.0470.4819-0.0470.332158.549317.412170.6024
151.43770.4482-1.26290.9231-0.84662.34810.3956-0.28060.05170.16-0.14260.1726-0.39570.3346-0.26080.43630.00520.02720.59030.02050.355550.625927.308167.7259
160.1660.0011-0.39520.9785-0.41321.18420.0921-0.0666-0.00910.45310.14840.0521-0.41150.5545-0.13280.39480.0187-0.02610.3101-0.0320.365932.910821.3887128.2453
170.8364-0.33850.1350.4916-0.42252.6152-0.01230.0955-0.4256-0.1941-0.09961.13650.4519-0.52290.16040.3251-0.04910.00380.3045-0.08120.554145.96625.3481129.7123
180.44490.55680.18321.50770.38260.1217-0.05470.1144-0.21820.6304-0.0745-1.13750.63920.51740.0760.69020.12990.01320.47710.03240.607730.9726.1395182.3173
190.23270.21140.12260.69790.50461.4207-0.07760.13140.1129-0.402-0.08920.2064-0.5225-1.31090.20790.54420.01530.00210.7709-0.05790.45543.33720.9162182.986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 136 through 282 )
2X-RAY DIFFRACTION2chain 'A' and (resid 283 through 349 )
3X-RAY DIFFRACTION3chain 'A' and (resid 350 through 478 )
4X-RAY DIFFRACTION4chain 'B' and (resid 135 through 293)
5X-RAY DIFFRACTION5chain 'B' and (resid 294 through 336 )
6X-RAY DIFFRACTION6chain 'B' and (resid 337 through 365 )
7X-RAY DIFFRACTION7chain 'B' and (resid 446 through 477 )
8X-RAY DIFFRACTION8chain 'C' and (resid 136 through 257)
9X-RAY DIFFRACTION9chain 'C' and (resid 258 through 336 )
10X-RAY DIFFRACTION10chain 'C' and (resid 337 through 478 )
11X-RAY DIFFRACTION11chain 'D' and (resid 136 through 293)
12X-RAY DIFFRACTION12chain 'D' and (resid 294 through 344 )
13X-RAY DIFFRACTION13chain 'D' and (resid 345 through 372 )
14X-RAY DIFFRACTION14chain 'D' and (resid 373 through 430 )
15X-RAY DIFFRACTION15chain 'D' and (resid 458 through 477 )
16X-RAY DIFFRACTION16chain 'F' and (resid -8 through 4 )
17X-RAY DIFFRACTION17chain 'E' and (resid -6 through 4)
18X-RAY DIFFRACTION18chain 'G' and (resid -6 through 4 )
19X-RAY DIFFRACTION19chain 'H' and (resid -8 through 4 )

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