+Open data
-Basic information
Entry | Database: PDB / ID: 5il2 | ||||||
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Title | Crystal structure of SAH-bound METTL3-METTL14 complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / 6-adenosine methylation / METTL3-METTL14 complex | ||||||
Function / homology | Function and homology information mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / RNA N6-methyladenosine methyltransferase complex / negative regulation of hematopoietic progenitor cell differentiation / mRNA m(6)A methyltransferase activity / positive regulation of cap-independent translational initiation / adenosine to inosine editing / endothelial to hematopoietic transition / RNA methyltransferase activity / regulation of meiotic cell cycle ...mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / RNA N6-methyladenosine methyltransferase complex / negative regulation of hematopoietic progenitor cell differentiation / mRNA m(6)A methyltransferase activity / positive regulation of cap-independent translational initiation / adenosine to inosine editing / endothelial to hematopoietic transition / RNA methyltransferase activity / regulation of meiotic cell cycle / primary miRNA processing / : / RNA methylation / forebrain radial glial cell differentiation / gliogenesis / dosage compensation by inactivation of X chromosome / S-adenosyl-L-methionine binding / regulation of hematopoietic stem cell differentiation / regulation of T cell differentiation / regulation of neuron differentiation / negative regulation of type I interferon-mediated signaling pathway / oogenesis / stem cell population maintenance / mRNA destabilization / negative regulation of Notch signaling pathway / mRNA catabolic process / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of translation / mRNA splicing, via spliceosome / mRNA processing / circadian rhythm / cellular response to UV / spermatogenesis / nuclear body / nuclear speck / protein heterodimerization activity / mRNA binding / innate immune response / DNA damage response / Golgi apparatus / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.606 Å | ||||||
Authors | Wang, X. / Guan, Z. / Zou, T. / Yin, P. | ||||||
Citation | Journal: Nature / Year: 2016 Title: Structural basis of N6-adenosine methylation by the METTL3-METTL14 complex Authors: Wang, X. / Feng, J. / Xue, Y. / Guan, Z. / Zhang, D. / Liu, Z. / Gong, Z. / Wang, Q. / Huang, J. / Tang, C. / Zou, T. / Yin, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5il2.cif.gz | 221.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5il2.ent.gz | 182.2 KB | Display | PDB format |
PDBx/mmJSON format | 5il2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/5il2 ftp://data.pdbj.org/pub/pdb/validation_reports/il/5il2 | HTTPS FTP |
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-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: 24427.109 Da / Num. of mol.: 1 / Fragment: UNP residues 369-580 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL3 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q86U44, mRNA (2'-O-methyladenosine-N6-)-methyltransferase | ||
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#2: Protein | Mass: 34794.402 Da / Num. of mol.: 1 / Fragment: UNP residues 109-408 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL14 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9HCE5, mRNA (2'-O-methyladenosine-N6-)-methyltransferase | ||
#3: Chemical | ChemComp-SAH / | ||
#4: Chemical | ChemComp-EDO / #5: 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: 2.66 Å3/Da / Density % sol: 53.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: PEG 8000, sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.606→45 Å / Num. obs: 79825 / % possible obs: 99.9 % / Redundancy: 13.2 % / Net I/σ(I): 21.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.606→38.247 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.606→38.247 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: 9.2913 Å / Origin y: 21.0225 Å / Origin z: 17.743 Å
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Refinement TLS group | Selection details: all |