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Yorodumi- PDB-8q9w: Crystal structure of HsRNMT complexed with sinefungin and GMP-PnP -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q9w | ||||||
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Title | Crystal structure of HsRNMT complexed with sinefungin and GMP-PnP | ||||||
Components | mRNA cap guanine-N7 methyltransferase | ||||||
Keywords | RNA BINDING PROTEIN / Methyl transferase | ||||||
Function / homology | Function and homology information mRNA cap methyltransferase RNMT:RAMAC complex / mRNA capping enzyme complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / 7-methylguanosine mRNA capping / cellular response to leukemia inhibitory factor / fibrillar center / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...mRNA cap methyltransferase RNMT:RAMAC complex / mRNA capping enzyme complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / 7-methylguanosine mRNA capping / cellular response to leukemia inhibitory factor / fibrillar center / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / receptor complex / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Petit, A.P. / Fyfe, P.K. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Structure-Guided Design of HsRNMT inhibitors Authors: Petit, A.P. / Fyfe, P.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q9w.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q9w.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 8q9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q9w_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8q9w_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8q9w_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 8q9w_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/8q9w ftp://data.pdbj.org/pub/pdb/validation_reports/q9/8q9w | HTTPS FTP |
-Related structure data
Related structure data | 8q69C 8q8gC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
#1: Protein | Mass: 32550.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNMT, KIAA0398 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O43148, mRNA (guanine-N7)-methyltransferase #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-GNP / | #5: 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: 2.2 Å3/Da / Density % sol: 44.05 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES pH 6.3-6.9, 50 mM Na2SO4, 18-25 % PEG 6000 PH range: 6.3-6.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2018 |
Radiation | Monochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→42.04 Å / Num. obs: 19534 / % possible obs: 99.8 % / Redundancy: 4.7 % / CC1/2: 0.98 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2178 / CC1/2: 0.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.04 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.41 / 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: 2.5→42.04 Å
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Refine LS restraints |
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LS refinement shell |
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