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Yorodumi- PDB-6kmr: Crystal structure of human N6amt1-Trm112 in complex with SAM (spa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kmr | |||||||||
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Title | Crystal structure of human N6amt1-Trm112 in complex with SAM (space group P6122) | |||||||||
Components |
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Keywords | TRANSFERASE / methyltransferase / complex / protein translation / polypeptide release factor eRF1 | |||||||||
Function / homology | Function and homology information histone H4K12 methyltransferase activity / eRF1 methyltransferase complex / protein-glutamine N-methyltransferase activity / arsonoacetate metabolic process / : / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / toxin metabolic process / site-specific DNA-methyltransferase (adenine-specific) activity ...histone H4K12 methyltransferase activity / eRF1 methyltransferase complex / protein-glutamine N-methyltransferase activity / arsonoacetate metabolic process / : / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / toxin metabolic process / site-specific DNA-methyltransferase (adenine-specific) activity / tRNA modification in the nucleus and cytosol / Methylation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / rRNA methylation / rRNA modification in the nucleus and cytosol / negative regulation of gene expression, epigenetic / Eukaryotic Translation Termination / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / positive regulation of cell growth / methylation / nucleic acid binding / 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 / Resolution: 2 Å | |||||||||
Authors | Li, W.J. / Shi, Y. / Zhang, T.L. / Ye, J. / Ding, J.P. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell Discov / Year: 2019 Title: Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase. Authors: Li, W. / Shi, Y. / Zhang, T. / Ye, J. / Ding, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kmr.cif.gz | 153 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kmr.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 6kmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kmr_validation.pdf.gz | 744.3 KB | Display | wwPDB validaton report |
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Full document | 6kmr_full_validation.pdf.gz | 747.3 KB | Display | |
Data in XML | 6kmr_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6kmr_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/6kmr ftp://data.pdbj.org/pub/pdb/validation_reports/km/6kmr | HTTPS FTP |
-Related structure data
Related structure data | 6kmsSC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 14346.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112, AD-001, HSPC152, HSPC170 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9UI30 |
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#2: Protein | Mass: 24597.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: N6AMT1, C21orf127, HEMK2, PRED28 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: Q9Y5N5, Transferases; Transferring one-carbon groups; Methyltransferases, site-specific DNA-methyltransferase (adenine-specific) |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-SAM / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 61.68 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M succinic acid, pH 7.0, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 25, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 31971 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.69 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.049 / Rrim(I) all: 0.125 / Χ2: 0.806 / Net I/σ(I): 4.3 / Num. measured all: 206280 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KMS Resolution: 2→42.026 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.51 Å2 / Biso mean: 37.9946 Å2 / Biso min: 15.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→42.026 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -43.6353 Å / Origin y: -14.944 Å / Origin z: -11.1306 Å
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Refinement TLS group |
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