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- PDB-8ipm: The structure of human mitochondrial methyltransferase METTL15 wi... -
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Open data
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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 | ||||||
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![]() | RIBOSOMAL PROTEIN / human mitochondrial methyltransferase METTL15 | ||||||
Function / homology | ![]() rRNA (cytosine-N4-)-methyltransferase activity / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA processing / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lv, M.Q. / Zhou, W.W. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.8 KB | Display | ![]() |
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PDB format | ![]() | 114.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 722 KB | Display | ![]() |
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Full document | ![]() | 724.1 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ipiC ![]() 8ipkC ![]() 8iplC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() 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.) ![]() |
#4: Chemical | ChemComp-SFG / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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