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Yorodumi- PDB-5ex0: Crystal structure of human SMYD3 in complex with a MAP3K2 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ex0 | |||||||||||||||||||||
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Title | Crystal structure of human SMYD3 in complex with a MAP3K2 peptide | |||||||||||||||||||||
Components |
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Keywords | TRANSFERASE / SET domain / methylation / chromatin / cancer | |||||||||||||||||||||
Function / homology | Function and homology information histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / mitogen-activated protein kinase kinase kinase / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / MAP kinase kinase kinase activity / cellular response to dexamethasone stimulus ...histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / mitogen-activated protein kinase kinase kinase / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / MAP kinase kinase kinase activity / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines / nucleosome assembly / cellular response to mechanical stimulus / positive regulation of peptidyl-serine phosphorylation / methylation / protein kinase activity / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||||||||||||||
Authors | Fu, W. / Liu, N. / Qiao, Q. / Wang, M. / Min, J. / Zhu, B. / Xu, R.M. / Yang, N. | |||||||||||||||||||||
Funding support | China, 6items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Basis for Substrate Preference of SMYD3, a SET Domain-containing Protein Lysine Methyltransferase Authors: Fu, W. / Liu, N. / Qiao, Q. / Wang, M. / Min, J. / Zhu, B. / Xu, R.M. / Yang, N. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ex0.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ex0.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ex0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/5ex0 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/5ex0 | HTTPS FTP |
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-Related structure data
Related structure data | 5ex3C 3mekS C: citing same article (ref.) 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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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AD
#1: Protein | Mass: 49541.492 Da / Num. of mol.: 1 / Mutation: K13N, K140R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD3, ZMYND1, ZNFN3A1 / Plasmid: pET28a-smt / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL References: UniProt: Q9H7B4, histone-lysine N-methyltransferase |
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#2: Protein/peptide | Mass: 1085.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y2U5*PLUS |
-Non-polymers , 4 types, 123 molecules
#3: Chemical | #4: Chemical | ChemComp-SAH / | #5: Chemical | #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: 3.25 Å3/Da / Density % sol: 62.2 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.4M NaAC |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 18908 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 40.89 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.049 / Rrim(I) all: 0.121 / Χ2: 0.928 / Net I/av σ(I): 15.755 / Net I/σ(I): 7.4 / Num. measured all: 113209 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MEK Resolution: 2.7→47.66 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.55 / Stereochemistry target values: ML Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.53 Å2 / Biso mean: 36.4011 Å2 / Biso min: 17.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→47.66 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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