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Open data
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Basic information
Entry | Database: PDB / ID: 5lgq | |||||||||
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Title | Crystal structure of mouse CARM1 in complex with ligand P2C3s | |||||||||
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![]() | TRANSFERASE / PROTEIN ARGININE METHYLTRANSFERASE / CATALYTIC DOMAIN / CHROMATIN REGULATOR / MRNA PROCESSING / MRNA SPLICING / NUCLEUS / S-ADENOSYL-L-METHIONINE / TRANSCRIPTION / TRANSCRIPTION REGULATION | |||||||||
Function / homology | ![]() 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 / endochondral bone morphogenesis / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / endochondral bone morphogenesis / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / type I protein arginine methyltransferase / negative regulation of dendrite development / Regulation of lipid metabolism by PPARalpha / protein-arginine omega-N asymmetric methyltransferase activity / Cytoprotection by HMOX1 / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / protein methyltransferase activity / Estrogen-dependent gene expression / Deadenylation of mRNA / regulation of intracellular estrogen receptor signaling pathway / protein-arginine N-methyltransferase activity / replication fork reversal / positive regulation of cytoplasmic translation / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / mRNA stabilization / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent 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 / estrogen receptor signaling pathway / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / nuclear receptor-mediated steroid hormone signaling pathway / protein localization to chromatin / response to cAMP / catalytic step 2 spliceosome / nuclear receptor coactivator activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA 3'-UTR binding / lysine-acetylated histone binding / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / 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 / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Marechal, N. / Troffer-Charlier, N. / Cura, V. / Bonnefond, L. / Cavarelli, J. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 821.1 KB | Display | ![]() |
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PDB format | ![]() | 702.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 58.4 KB | Display | |
Data in CIF | ![]() | 84.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lgpC ![]() 5lgrC ![]() 5lgsC ![]() 5ih3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 8 molecules ABCDFEGH
#1: Protein | Mass: 40850.457 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9WVG6, type I protein arginine methyltransferase #2: Protein/peptide | Mass: 1172.375 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 7 types, 857 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/DXE.gif)
![](data/chem/img/PG6.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/8ZB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/DXE.gif)
![](data/chem/img/PG6.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/8ZB.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-DXE / | #6: Chemical | ChemComp-PG6 / | #7: Chemical | ChemComp-SO4 / | #8: Chemical | ChemComp-8ZB / ( #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.89 % |
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Crystal grow | Temperature: 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. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.073 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→48.152 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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