+Open data
-Basic information
Entry | Database: PDB / ID: 6jat | ||||||
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Title | Crystal structure of SETD3 bound to Actin peptide and SFG | ||||||
Components |
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Keywords | TRANSFERASE / SET domain | ||||||
Function / homology | Function and homology information protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / dynactin complex / histone H3K36 methyltransferase activity / myosin filament / histone H3K4 methyltransferase activity / mesenchyme migration ...protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / dynactin complex / histone H3K36 methyltransferase activity / myosin filament / histone H3K4 methyltransferase activity / mesenchyme migration / positive regulation of muscle cell differentiation / Smooth Muscle Contraction / filopodium / muscle contraction / cell periphery / PKMTs methylate histone lysines / lamellipodium / actin binding / cell body / blood microparticle / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromatin / positive regulation of gene expression / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.713 Å | ||||||
Authors | Li, H. / Zheng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: to be published Title: Crystal structure of SETD3 bound to Actin peptide and SFG Authors: Li, H. / Zheng, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jat.cif.gz | 211.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jat.ent.gz | 166.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/6jat ftp://data.pdbj.org/pub/pdb/validation_reports/ja/6jat | HTTPS FTP |
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-Related structure data
Related structure data | 3smtS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein | Mass: 57223.000 Da / Num. of mol.: 2 / Fragment: SETD3 protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETD3, C14orf154 / Plasmid: pSUMOH10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q86TU7, histone-lysine N-methyltransferase #2: Protein/peptide | Mass: 2573.942 Da / Num. of mol.: 2 / Fragment: Actin peptide / Source method: obtained synthetically / Details: chemical synthesized peptide 60-81 / Source: (synth.) Homo sapiens (human) / References: UniProt: P63267 |
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-Non-polymers , 4 types, 92 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.66 % / Mosaicity: 0.778 ° / Mosaicity esd: 0.006 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M HEPES/Sodium hydroxide, 0.2 M Ammonium sulfate, 20% PEG 8000, 10% 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 29, 2018 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 38336 / % possible obs: 99.8 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.055 / Rrim(I) all: 0.172 / Χ2: 0.862 / Net I/σ(I): 4.4 / Num. measured all: 370511 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.545
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SMT Resolution: 2.713→49.74 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 93.45 Å2 / Biso mean: 46.2428 Å2 / Biso min: 24.52 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.713→49.74 Å
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