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Yorodumi- PDB-1or8: Structure of the Predominant protein arginine methyltransferase PRMT1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1or8 | ||||||
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Title | Structure of the Predominant protein arginine methyltransferase PRMT1 | ||||||
Components |
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Keywords | TRANSFERASE / protein arginine methylation / AdoMet-dependent methylation | ||||||
Function / homology | Function and homology information snoRNP binding / peptidyl-arginine omega-N-methylation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Estrogen-dependent gene expression / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / positive regulation of hemoglobin biosynthetic process / Extra-nuclear estrogen signaling / protein-arginine omega-N monomethyltransferase activity / N-methyltransferase activity ...snoRNP binding / peptidyl-arginine omega-N-methylation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Estrogen-dependent gene expression / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / positive regulation of hemoglobin biosynthetic process / Extra-nuclear estrogen signaling / protein-arginine omega-N monomethyltransferase activity / N-methyltransferase activity / histone H4R3 methyltransferase activity / regulation of BMP signaling pathway / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / protein methyltransferase activity / methylosome / protein methylation / protein-arginine N-methyltransferase activity / S-adenosyl-L-methionine binding / negative regulation of JNK cascade / cardiac muscle tissue development / methyl-CpG binding / positive regulation of p38MAPK cascade / mitogen-activated protein kinase p38 binding / histone methyltransferase activity / negative regulation of megakaryocyte differentiation / S-adenosylmethionine-dependent methyltransferase activity / RNA splicing / positive regulation of erythrocyte differentiation / liver regeneration / positive regulation of translation / protein homooligomerization / neuron projection development / in utero embryonic development / positive regulation of cell population proliferation / enzyme binding / protein-containing complex / nucleoplasm / nucleus / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Zhang, X. / Cheng, X. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structure of the Predominant Protein Arginine Methyltransferase PRMT1 and Analysis of Its Binding to Substrate Peptides Authors: Zhang, X. / Cheng, X. | ||||||
History |
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Remark 400 | THE ENTRY PRESENTS A STRUCTURE OF A COMPLEX BETWEEN PROTEIN ARGININE N-METHYLTRANSFERASE 1 AND ...THE ENTRY PRESENTS A STRUCTURE OF A COMPLEX BETWEEN PROTEIN ARGININE N-METHYLTRANSFERASE 1 AND SUBSTRATE PEPTIDE (19 RESIDUES). THE COORDINATES PRESENTED IN THE FILE FOR PEPTIDE SUBSTRATE ARE FOR FOUR POSSIBLE ALTERNATE LOCATION AS CHAINS B, C, D AND E. REMARKS 465, 470 AND SHORT CONTACTS SHOULD BE VIEWED IN THIS CONTEXT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1or8.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1or8.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 1or8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/1or8 ftp://data.pdbj.org/pub/pdb/validation_reports/or/1or8 | HTTPS FTP |
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-Related structure data
Related structure data | 1orhC 1oriC 1f3lS 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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1 |
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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 5 molecules ABCDE
#1: Protein | Mass: 39267.855 Da / Num. of mol.: 1 / Fragment: S14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: HRMT1L2 OR PRMT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63009, EC: 2.1.1.125 |
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#2: Protein/peptide | Mass: 1672.792 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: chemically synthesized |
-Non-polymers , 4 types, 174 molecules
#3: Chemical | ChemComp-SAH / | ||
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#4: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.55 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 4.7 Details: ammonium phosphate, pH 4.7, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: May 18, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→25 Å / Num. all: 22428 / Num. obs: 22428 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.455 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.35→2.39 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.2 / Num. unique all: 691 / % possible all: 61.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F3L Resolution: 2.35→24.65 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 34.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→24.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.46 Å / Rfactor Rfree error: 0.03
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