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Yorodumi- PDB-8ipi: The apo structure of human mitochondrial methyltransferase METTL15 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ipi | ||||||
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Title | The apo structure of human mitochondrial methyltransferase METTL15 | ||||||
Components | 12S rRNA N4-methylcytidine (m4C) methyltransferase | ||||||
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 / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 8ipi.cif.gz | 129.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ipi.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ipi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/8ipi ftp://data.pdbj.org/pub/pdb/validation_reports/ip/8ipi | HTTPS FTP |
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-Related structure data
Related structure data | 8ipkC 8iplC 8ipmC 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 | 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 |
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#2: 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: 2.59 Å3/Da / Density % sol: 52.55 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 10% PEG MME 2000, 0.2M Ammonium sulfate, 0.1 M sodium acetate (pH 5.5) |
-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: Jul 24, 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: 2.1→31.34 Å / Num. obs: 23694 / % possible obs: 100 % / Redundancy: 17.9 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1134 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→31.336 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.82 / 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: 2.1→31.336 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 26.4696 Å / Origin y: -26.3576 Å / Origin z: -7.8066 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 8 through 338) |