+Open data
-Basic information
Entry | Database: PDB / ID: 6d2l | ||||||
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Title | Crystal structure of human CARM1 with (S)-SKI-72 | ||||||
Components | Histone-arginine methyltransferase CARM1 | ||||||
Keywords | TRANSFERASE/INHIBITOR / CARM1 / PRMT4 / SKI-72 inhibitor / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information : / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methyltransferase activity / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal ...: / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methyltransferase activity / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / positive regulation of epithelial cell apoptotic process / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / nuclear replication fork / positive regulation of fat cell differentiation / 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 / lysine-acetylated histone binding / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / RMTs methylate histone arginines / Transcriptional regulation of white adipocyte differentiation / Circadian Clock / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | DONG, A. / ZENG, H. / WALKER, J.R. / Hutchinson, A. / Seitova, A. / LUO, M. / CAI, X.C. / KE, W. / WANG, J. / SHI, C. ...DONG, A. / ZENG, H. / WALKER, J.R. / Hutchinson, A. / Seitova, A. / LUO, M. / CAI, X.C. / KE, W. / WANG, J. / SHI, C. / ZHENG, W. / LEE, J.P. / IBANEZ, G. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Elife / Year: 2019 Title: A chemical probe of CARM1 alters epigenetic plasticity against breast cancer cell invasion. Authors: Cai, X.C. / Zhang, T. / Kim, E.J. / Jiang, M. / Wang, K. / Wang, J. / Chen, S. / Zhang, N. / Wu, H. / Li, F. / Dela Sena, C.C. / Zeng, H. / Vivcharuk, V. / Niu, X. / Zheng, W. / Lee, J.P. / ...Authors: Cai, X.C. / Zhang, T. / Kim, E.J. / Jiang, M. / Wang, K. / Wang, J. / Chen, S. / Zhang, N. / Wu, H. / Li, F. / Dela Sena, C.C. / Zeng, H. / Vivcharuk, V. / Niu, X. / Zheng, W. / Lee, J.P. / Chen, Y. / Barsyte, D. / Szewczyk, M. / Hajian, T. / Ibanez, G. / Dong, A. / Dombrovski, L. / Zhang, Z. / Deng, H. / Min, J. / Arrowsmith, C.H. / Mazutis, L. / Shi, L. / Vedadi, M. / Brown, P.J. / Xiang, J. / Qin, L.X. / Xu, W. / Luo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d2l.cif.gz | 417.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d2l.ent.gz | 339.8 KB | Display | PDB format |
PDBx/mmJSON format | 6d2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/6d2l ftp://data.pdbj.org/pub/pdb/validation_reports/d2/6d2l | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 38976.453 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 References: UniProt: Q86X55, type I protein arginine methyltransferase |
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-Non-polymers , 5 types, 775 molecules
#2: Chemical | ChemComp-FTG / ( #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.35 Å3/Da / Density % sol: 47.75 % / Mosaicity: 0.704 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 3350, 0.2 M NH4SO4, 0.1 M HEPES pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 142452 / % possible obs: 97 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.081 / Rrim(I) all: 0.176 / Χ2: 0.83 / Net I/σ(I): 4.1 / Num. measured all: 640160 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 2→50.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.978 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.96 Å2 / Biso mean: 29.578 Å2 / Biso min: 10.24 Å2
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Refinement step | Cycle: final / Resolution: 2→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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