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Yorodumi- PDB-5l6d: Crystal structure of the human METTL3-METTL14 complex bound to SAH -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l6d | ||||||
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Title | Crystal structure of the human METTL3-METTL14 complex bound to SAH | ||||||
Components | (N6-adenosine-methyltransferase ...) x 2 | ||||||
Keywords | TRANSFERASE / RNA methyltransferase N6-adenine methylation Rossmann fold | ||||||
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 / RNA methylation / primary miRNA processing / : / 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: 1.852 Å | ||||||
Authors | Sledz, P. / Jinek, M. | ||||||
Citation | Journal: Elife / Year: 2016 Title: Structural insights into the molecular mechanism of the m(6)A writer complex. Authors: Sledz, P. / Jinek, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l6d.cif.gz | 186.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l6d.ent.gz | 154.4 KB | Display | PDB format |
PDBx/mmJSON format | 5l6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/5l6d ftp://data.pdbj.org/pub/pdb/validation_reports/l6/5l6d | 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
-N6-adenosine-methyltransferase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 25886.646 Da / Num. of mol.: 1 / Fragment: UNP residues 354-580 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL3, MTA70 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q86U44, mRNA (2'-O-methyladenosine-N6-)-methyltransferase |
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#2: Protein | Mass: 33490.051 Da / Num. of mol.: 1 / Fragment: UNP residues 107-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL14, KIAA1627 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9HCE5, mRNA (2'-O-methyladenosine-N6-)-methyltransferase |
-Non-polymers , 4 types, 402 molecules
#3: Chemical | ChemComp-SAH / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-ACT / |
#6: 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: 2.23 Å3/Da / Density % sol: 44.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 3350, 300 mM Mg acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.03965 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03965 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→49.65 Å / Num. all: 87473 / Num. obs: 46603 / % possible obs: 99.9 % / Redundancy: 19.5 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 34.19 |
Reflection shell | Resolution: 1.85→1.96 Å / Redundancy: 19.3 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 4.91 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.852→49.634 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.66 / 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: 1.852→49.634 Å
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Refine LS restraints |
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LS refinement shell |
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