+Open data
-Basic information
Entry | Database: PDB / ID: 7faj | ||||||
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Title | CARM1 bound with compound 43 | ||||||
Components | Histone-arginine methyltransferase CARM1 | ||||||
Keywords | TRANSFERASE / Histone-arginine methyltransferase CARM1 | ||||||
Function / homology | Function and homology information histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / negative regulation of dendrite development / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity ...histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / negative regulation of dendrite development / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / positive regulation of epithelial cell apoptotic process / positive regulation of fat cell differentiation / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / nuclear replication fork / lysine-acetylated histone binding / response to cAMP / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / PPARA activates gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / RMTs methylate histone arginines / beta-catenin binding / Circadian Clock / DNA-binding transcription factor binding / methylation / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / positive regulation of cell population proliferation / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24507255823 Å | ||||||
Authors | Cao, D.Y. / Li, J. / Xiong, B. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structure-Based Discovery of Potent CARM1 Inhibitors for Solid Tumor and Cancer Immunology Therapy. Authors: Zhang, Z. / Guo, Z. / Xu, X. / Cao, D. / Yang, H. / Li, Y. / Shi, Q. / Du, Z. / Guo, X. / Wang, X. / Chen, D. / Zhang, Y. / Chen, L. / Zhou, K. / Li, J. / Geng, M. / Huang, X. / Xiong, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7faj.cif.gz | 336.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7faj.ent.gz | 221.3 KB | Display | PDB format |
PDBx/mmJSON format | 7faj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/7faj ftp://data.pdbj.org/pub/pdb/validation_reports/fa/7faj | HTTPS FTP |
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-Related structure data
Related structure data | 7faiC 6izqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 38228.598 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q86X55, type I protein arginine methyltransferase #2: Chemical | ChemComp-XJ4 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 22-27% PEG 3350, 0.15M sodium malate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.24507255823→75.3 Å / Num. obs: 74529 / % possible obs: 99.3 % / Redundancy: 13.6 % / Biso Wilson estimate: 36.9000070658 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.25→2.3 Å / Rmerge(I) obs: 0.656 / Num. unique obs: 74529 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IZQ Resolution: 2.24507255823→60.9248 Å / SU ML: 0.259406702227 / Cross valid method: NONE / σ(F): 1.3418418283 / Phase error: 26.095902159 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.7674088481 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24507255823→60.9248 Å
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Refine LS restraints |
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LS refinement shell |
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