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- PDB-6v62: SETD3 double mutant (N255F/W273A) in Complex with an Actin Peptid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6v62 | ||||||
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Title | SETD3 double mutant (N255F/W273A) in Complex with an Actin Peptide with His73 Replaced with Lysine | ||||||
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![]() | TRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex | ||||||
Function / homology | ![]() basal body patch / protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / tight junction assembly / regulation of transepithelial transport / morphogenesis of a polarized epithelium / profilin binding ...basal body patch / protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / tight junction assembly / regulation of transepithelial transport / morphogenesis of a polarized epithelium / profilin binding / protein localization to bicellular tight junction / structural constituent of postsynaptic actin cytoskeleton / dense body / Formation of annular gap junctions / histone H3K36 methyltransferase activity / Gap junction degradation / Cell-extracellular matrix interactions / regulation of stress fiber assembly / Adherens junctions interactions / histone H3K4 methyltransferase activity / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of synaptic vesicle endocytosis / apical junction complex / regulation of focal adhesion assembly / sarcomere organization / positive regulation of wound healing / myofibril / maintenance of blood-brain barrier / positive regulation of muscle cell differentiation / NuA4 histone acetyltransferase complex / filamentous actin / Recycling pathway of L1 / calyx of Held / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / RHOBTB2 GTPase cycle / phagocytic vesicle / EPHB-mediated forward signaling / axonogenesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / cell motility / RHO GTPases Activate Formins / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Signaling by high-kinase activity BRAF mutants / PKMTs methylate histone lysines / MAP2K and MAPK activation / Schaffer collateral - CA1 synapse / structural constituent of cytoskeleton / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / platelet aggregation / VEGFA-VEGFR2 Pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / cell-cell junction / Clathrin-mediated endocytosis / actin binding / angiogenesis / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / blood microparticle / cytoskeleton / positive regulation of cell migration / hydrolase activity / axon / focal adhesion / ubiquitin protein ligase binding / synapse / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / protein kinase binding / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dai, S. / Horton, J.R. / Cheng, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An engineered variant of SETD3 methyltransferase alters target specificity from histidine to lysine methylation. Authors: Dai, S. / Horton, J.R. / Wilkinson, A.W. / Gozani, O. / Zhang, X. / Cheng, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.6 KB | Display | ![]() |
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PDB format | ![]() | 90.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 345.8 KB | Display | ![]() |
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Full document | ![]() | 346.3 KB | Display | |
Data in XML | ![]() | 1.6 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v63C ![]() 6mbjS 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
#1: Protein/peptide | Mass: 2859.280 Da / Num. of mol.: 1 / Mutation: H73K / Source method: obtained synthetically / Source: (synth.) ![]() | ||||
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#2: Protein | Mass: 67404.117 Da / Num. of mol.: 1 / Mutation: N255F, W273A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q86TU7, protein-histidine N-methyltransferase | ||||
#3: Chemical | ChemComp-SAH / | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.85 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 24952 / % possible obs: 96 % / Redundancy: 5.7 % / Biso Wilson estimate: 31.61 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.08 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 4.2 % / Num. unique obs: 2284 / CC1/2: 0.529 / % possible all: 89.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6MBJ Resolution: 2.36→39.49 Å / SU ML: 0.3271 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.0706
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→39.49 Å
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Refine LS restraints |
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LS refinement shell |
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