+Open data
-Basic information
Entry | Database: PDB / ID: 6gfn | ||||||
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Title | METTL16 MTase domain | ||||||
Components | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | ||||||
Keywords | TRANSFERASE / RNA SAM methyltransferase | ||||||
Function / homology | Function and homology information snRNA (adenine-N6)-methylation / negative regulation of 3'-UTR-mediated mRNA stabilization / U6 snRNA m6A methyltransferase / U6 snRNA (adenine-(43)-N(6))-methyltransferase activity / 23S rRNA (adenine(1618)-N(6))-methyltransferase activity / U6 snRNA 3'-end binding / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / S-adenosylmethionine biosynthetic process / : ...snRNA (adenine-N6)-methylation / negative regulation of 3'-UTR-mediated mRNA stabilization / U6 snRNA m6A methyltransferase / U6 snRNA (adenine-(43)-N(6))-methyltransferase activity / 23S rRNA (adenine(1618)-N(6))-methyltransferase activity / U6 snRNA 3'-end binding / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / S-adenosylmethionine biosynthetic process / : / rRNA base methylation / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / mRNA destabilization / mRNA catabolic process / RNA stem-loop binding / RNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å | ||||||
Authors | Chen, K.M. / Mendel, M. / Homolka, D. / McCarthy, A.A. / Pillai, R.S. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Mol. Cell / Year: 2018 Title: Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development. Authors: Mendel, M. / Chen, K.M. / Homolka, D. / Gos, P. / Pandey, R.R. / McCarthy, A.A. / Pillai, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gfn.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gfn.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 6gfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/6gfn ftp://data.pdbj.org/pub/pdb/validation_reports/gf/6gfn | HTTPS FTP |
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-Related structure data
Related structure data | 6gfkSC 6gt5C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/578 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33345.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL16, METT10D / Plasmid: pETM-11-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q86W50, U6 snRNA m6A methyltransferase, mRNA (2'-O-methyladenosine-N6-)-methyltransferase |
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#2: Chemical | ChemComp-SAH / |
#3: 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: 57.6 % / Description: Rod shaped crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M di-sodium tartrate and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 2, 2018 / Details: Be CRL and multilayer mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→82.24 Å / Num. obs: 5724 / % possible obs: 93.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 95.61 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.073 / Rrim(I) all: 0.192 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.85→3.2 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.32 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 286 / CC1/2: 0.59 / Rpim(I) all: 0.5 / Rrim(I) all: 1.42 / % possible all: 78.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GFK Resolution: 2.86→82.23 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.446
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Displacement parameters | Biso mean: 93.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.86→82.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.86→3.31 Å / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 4.3006 Å / Origin y: -21.606 Å / Origin z: -14.6035 Å
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Refinement TLS group | Selection details: { A|1 - A|300 } |