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Open data
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Basic information
Entry | Database: PDB / ID: 7cv6 | ||||||
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Title | RNA methyltransferase METTL4 | ||||||
![]() | Methyltransferase-like protein 2 | ||||||
![]() | NUCLEAR PROTEIN / RNA methyltransferase | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luo, Q. / Ma, J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.5 KB | Display | ![]() |
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PDB format | ![]() | 66.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cv7C ![]() 7cv8C ![]() 7cv9C ![]() 7cvaC ![]() 5il2S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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 | Mass: 47955.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8LFA9, Transferases; Transferring one-carbon groups; Methyltransferases | ||||
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#2: Chemical | ChemComp-SAH / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.49 Å3/Da / Density % sol: 72.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.49 M NaH2PO4 and 0.91 M K2HPO4, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→30 Å / Num. obs: 14468 / % possible obs: 82.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.049 / Rrim(I) all: 0.132 / Χ2: 1.017 / Net I/σ(I): 6.3 / Num. measured all: 83220 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5IL2 Resolution: 3.01→30 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.862 / SU B: 23.18 / SU ML: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 233.08 Å2 / Biso mean: 92.298 Å2 / Biso min: 11.19 Å2
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Refinement step | Cycle: final / Resolution: 3.01→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.01→3.083 Å / Rfactor Rfree error: 0
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