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- PDB-5l6e: Crystal structure of the human METTL3-METTL14 complex bound to SAM -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l6e | ||||||
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Title | Crystal structure of the human METTL3-METTL14 complex bound to SAM | ||||||
![]() | (N6-adenosine-methyltransferase ...) x 2 | ||||||
![]() | TRANSFERASE / methyltransferase N6-adenine methylation m6A Rossmann fold | ||||||
Function / homology | ![]() negative regulation of hematopoietic progenitor cell differentiation / mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / adenosine to inosine editing / RNA methyltransferase activity / endothelial to hematopoietic transition / RNA methylation ...negative regulation of hematopoietic progenitor cell differentiation / mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / adenosine to inosine editing / RNA methyltransferase activity / endothelial to hematopoietic transition / RNA methylation / regulation of meiotic cell cycle / primary miRNA processing / dosage compensation by inactivation of X chromosome / : / forebrain radial glial cell differentiation / S-adenosyl-L-methionine binding / gliogenesis / mRNA stabilization / regulation of hematopoietic stem cell differentiation / regulation of T cell differentiation / regulation of neuron differentiation / negative regulation of type I interferon-mediated signaling pathway / stem cell population maintenance / oogenesis / mRNA destabilization / negative regulation of Notch signaling pathway / mRNA catabolic process / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of translation / mRNA processing / mRNA splicing, via spliceosome / circadian rhythm / cellular response to UV / spermatogenesis / nuclear body / nuclear speck / protein heterodimerization activity / innate immune response / mRNA binding / DNA damage response / Golgi apparatus / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sledz, P. / Jinek, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189 KB | Display | ![]() |
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PDB format | ![]() | 148.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 730.1 KB | Display | ![]() |
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Full document | ![]() | 733.4 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 31.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l6dSC 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
-N6-adenosine-methyltransferase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 25886.646 Da / Num. of mol.: 1 / Fragment: UNP residues 90-580 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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.) ![]() ![]() ![]() References: UniProt: Q9HCE5, mRNA (2'-O-methyladenosine-N6-)-methyltransferase |
-Non-polymers , 4 types, 361 molecules ![](data/chem/img/SAM.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SAM / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-ACT / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.19 % |
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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: ![]() ![]() ![]() |
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: 1.9→44.62 Å / Num. obs: 43352 / % possible obs: 99.9 % / Redundancy: 19.5 % / CC1/2: 1 / Rsym value: 0.089 / Net I/σ(I): 29.93 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 4.71 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5L6D Resolution: 1.901→44.611 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.2 / 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: 1.901→44.611 Å
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Refine LS restraints |
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LS refinement shell |
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