[English] 日本語
Yorodumi- PDB-6h2v: Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h2v | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA m6A1832 methyltransferase at 2.5A resolution | |||||||||
Components |
| |||||||||
Keywords | TRANSFERASE / rRNA maturation / methyltransferase / translation / ribosome synthesis | |||||||||
Function / homology | Function and homology information rRNA (adenine-N6-)-methyltransferase activity / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / tRNA modification in the nucleus and cytosol / Methylation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / S-adenosyl-L-methionine binding ...rRNA (adenine-N6-)-methyltransferase activity / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / tRNA modification in the nucleus and cytosol / Methylation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / S-adenosyl-L-methionine binding / rRNA methylation / rRNA modification in the nucleus and cytosol / Eukaryotic Translation Termination / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / cell projection / positive regulation of translation / stem cell differentiation / presynapse / transferase activity / nucleic acid binding / postsynapse / protein heterodimerization activity / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å | |||||||||
Authors | van Tran, N. / Graille, M. | |||||||||
Funding support | France, 2items
| |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112. Authors: van Tran, N. / Ernst, F.G.M. / Hawley, B.R. / Zorbas, C. / Ulryck, N. / Hackert, P. / Bohnsack, K.E. / Bohnsack, M.T. / Jaffrey, S.R. / Graille, M. / Lafontaine, D.L.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6h2v.cif.gz | 274.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6h2v.ent.gz | 222.4 KB | Display | PDB format |
PDBx/mmJSON format | 6h2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h2v_validation.pdf.gz | 1007.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6h2v_full_validation.pdf.gz | 998.4 KB | Display | |
Data in XML | 6h2v_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 6h2v_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/6h2v ftp://data.pdbj.org/pub/pdb/validation_reports/h2/6h2v | HTTPS FTP |
-Related structure data
Related structure data | 6h2uSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 24581.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL5, DC3, HSPC133 / Production host: Escherichia coli (E. coli) References: UniProt: Q9NRN9, Transferases; Transferring one-carbon groups; Methyltransferases #2: Protein | Mass: 14291.479 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112, AD-001, HSPC152, HSPC170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI30 |
---|
-Non-polymers , 6 types, 42 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-PEG / | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.96 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 25% PEG 4,000; 0.2 M ammonium sulfate; 100 mM Na citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97996 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97996 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. obs: 36060 / % possible obs: 99.8 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.144 / Net I/σ(I): 14.05 |
Reflection shell | Resolution: 2.49→2.65 Å / CC1/2: 0.747 / % possible all: 99 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H2U Resolution: 2.49→49.77 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.888 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.309 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.306 / SU Rfree Blow DPI: 0.232 / SU Rfree Cruickshank DPI: 0.235
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 182.33 Å2 / Biso mean: 75.81 Å2 / Biso min: 43.04 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.37 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.49→49.77 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.49→2.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|