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Yorodumi- PDB-6ox0: SETD3 in Complex with an Actin Peptide with Sinefungin Replacing ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ox0 | ||||||
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Title | SETD3 in Complex with an Actin Peptide with Sinefungin Replacing SAH as Cofactor | ||||||
Components |
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Keywords | TRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex | ||||||
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 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex ...protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / nBAF complex / protein localization to adherens junction / brahma complex / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / dense body / Formation of annular gap junctions / regulation of G0 to G1 transition / histone H3K36 methyltransferase activity / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / adherens junction assembly / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOF GTPase cycle / Regulation of MITF-M-dependent genes involved in pigmentation / Adherens junctions interactions / tight junction / histone H3K4 methyltransferase activity / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / maintenance of blood-brain barrier / cortical cytoskeleton / positive regulation of muscle cell differentiation / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / EPHB-mediated forward signaling / substantia nigra development / axonogenesis / negative regulation of protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / cell motility / RHO GTPases Activate Formins / positive regulation of cell differentiation / adherens junction / FCGR3A-mediated phagocytosis / regulation of transmembrane transporter activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Signaling by high-kinase activity BRAF mutants / DNA Damage Recognition in GG-NER / PKMTs methylate histone lysines / MAP2K and MAPK activation / B-WICH complex positively regulates rRNA expression / tau protein binding / Schaffer collateral - CA1 synapse / structural constituent of cytoskeleton / kinetochore / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / VEGFA-VEGFR2 Pathway / nuclear matrix / cytoplasmic ribonucleoprotein granule / 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 / UCH proteinases / nucleosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.755 Å | ||||||
Authors | Horton, J.R. / Dai, S. / Cheng, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural basis for the target specificity of actin histidine methyltransferase SETD3. Authors: Dai, S. / Horton, J.R. / Woodcock, C.B. / Wilkinson, A.W. / Zhang, X. / Gozani, O. / Cheng, X. #1: Journal: Nature / Year: 2019 Title: SETD3 is an actin histidine methyltransferase that prevents primary dystocia. Authors: Wilkinson, A.W. / Diep, J. / Dai, S. / Liu, S. / Ooi, Y.S. / Song, D. / Li, T.M. / Horton, J.R. / Zhang, X. / Liu, C. / Trivedi, D.V. / Ruppel, K.M. / Vilches-Moure, J.G. / Casey, K.M. / ...Authors: Wilkinson, A.W. / Diep, J. / Dai, S. / Liu, S. / Ooi, Y.S. / Song, D. / Li, T.M. / Horton, J.R. / Zhang, X. / Liu, C. / Trivedi, D.V. / Ruppel, K.M. / Vilches-Moure, J.G. / Casey, K.M. / Mak, J. / Cowan, T. / Elias, J.E. / Nagamine, C.M. / Spudich, J.A. / Cheng, X. / Carette, J.E. / Gozani, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ox0.cif.gz | 433.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ox0.ent.gz | 349.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ox0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ox0_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6ox0_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6ox0_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 6ox0_validation.cif.gz | 62.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/6ox0 ftp://data.pdbj.org/pub/pdb/validation_reports/ox/6ox0 | HTTPS FTP |
-Related structure data
Related structure data | 6ox1C 6ox2C 6ox3C 6ox4C 6ox5C 6mbjS 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1788.008 Da / Num. of mol.: 2 / Fragment: residues 66-80 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P60709 #2: Protein | Mass: 67753.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETD3, C14orf154 / Production host: Escherichia coli (E. coli) References: UniProt: Q86TU7, protein-histidine N-methyltransferase #3: Chemical | #4: Chemical | ChemComp-EDO / #5: 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: 3.04 Å3/Da / Density % sol: 59.49 % |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→36.49 Å / Num. obs: 132568 / % possible obs: 98 % / Redundancy: 15.9 % / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.033 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.695 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 12128 / CC1/2: 0.627 / Rpim(I) all: 0.444 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MBJ Resolution: 1.755→36.486 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.755→36.486 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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