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Yorodumi- PDB-8ipm: The structure of human mitochondrial methyltransferase METTL15 wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ipm | ||||||
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Title | The structure of human mitochondrial methyltransferase METTL15 with h44_RNA, RBFA and SAM | ||||||
Components |
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Keywords | RIBOSOMAL PROTEIN / human mitochondrial methyltransferase METTL15 | ||||||
Function / homology | Function and homology information rRNA (cytosine-N4-)-methyltransferase activity / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA processing / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Lv, M.Q. / Zhou, W.W. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Discov / Year: 2024 Title: Structural insights into the specific recognition of mitochondrial ribosome-binding factor hsRBFA and 12 S rRNA by methyltransferase METTL15. Authors: Lv, M. / Zhou, W. / Hao, Y. / Li, F. / Zhang, H. / Yao, X. / Shi, Y. / Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ipm.cif.gz | 151.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ipm.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ipm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/8ipm ftp://data.pdbj.org/pub/pdb/validation_reports/ip/8ipm | HTTPS FTP |
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-Related structure data
Related structure data | 8ipiC 8ipkC 8iplC 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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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3815.315 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBFA, C18orf22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N0V3 |
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#2: Protein | Mass: 37768.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL15, METT5D1 / Production host: Escherichia coli (E. coli) References: UniProt: A6NJ78, Transferases; Transferring one-carbon groups; Methyltransferases |
#3: RNA chain | Mass: 6067.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#4: Chemical | ChemComp-SFG / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.23 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000, 0.2 M ADA (pH 6.4) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→33.53 Å / Num. obs: 8176 / % possible obs: 97.42 % / Redundancy: 9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 3.1→3.21 Å / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 888 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→33.528 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.32 / 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: 3.1→33.528 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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