+Open data
-Basic information
Entry | Database: PDB / ID: 7cv8 | ||||||
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Title | RNA methyltransferase METTL4 | ||||||
Components | Methyltransferase-like protein 2 | ||||||
Keywords | NUCLEAR PROTEIN / RNA methyltransferase | ||||||
Function / homology | Function and homology information RNA methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) activity / nucleic acid metabolic process / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / nucleic acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.37 Å | ||||||
Authors | Luo, Q. / Ma, J. | ||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Structural insights into molecular mechanism for N6-adenosine methylation by MT-A70 family methyltransferase METTL4 Authors: Luo, Q. / Mo, J. / Chen, H. / Hu, Z. / Wang, B. / Wu, J. / Liang, Z. / Xie, W. / Du, K. / Peng, M. / Li, Y. / Li, T. / Zhang, Y. / Shi, X. / Shen, W.H. / Shi, Y. / Dong, A. / Wang, H. / Ma, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cv8.cif.gz | 156.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cv8.ent.gz | 121.8 KB | Display | PDB format |
PDBx/mmJSON format | 7cv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cv8_validation.pdf.gz | 672.4 KB | Display | wwPDB validaton report |
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Full document | 7cv8_full_validation.pdf.gz | 676.5 KB | Display | |
Data in XML | 7cv8_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 7cv8_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/7cv8 ftp://data.pdbj.org/pub/pdb/validation_reports/cv/7cv8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47955.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g19340, F18O14.6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8LFA9, Transferases; Transferring one-carbon groups; Methyltransferases | ||||
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#2: Chemical | ChemComp-SFG / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.17 Å3/Da / Density % sol: 43.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1M Lithium chloride 0.1M HEPES pH 7.0 10% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→46.96 Å / Num. obs: 17743 / % possible obs: 98.8 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.054 / Rrim(I) all: 0.188 / Χ2: 1.95 / Net I/σ(I): 4.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.37→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.389 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.86 Å2 / Biso mean: 45.712 Å2 / Biso min: 21.42 Å2
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Refinement step | Cycle: final / Resolution: 2.37→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.37→2.428 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 9.0771 Å / Origin y: -13.8904 Å / Origin z: -25.0065 Å
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