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Yorodumi- PDB-5yko: Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yko | ||||||
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Title | Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide | ||||||
Components |
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Keywords | GENE REGULATION / JMJ14 / jumonji domain / C5HC2 zinc finger / H3K4me3 demethylase | ||||||
Function / homology | Function and homology information regulation of post-transcriptional gene silencing / : / L-pipecolic acid biosynthetic process / : / : / positive regulation of systemic acquired resistance / plant organ development / : / negative regulation of long-day photoperiodism, flowering / regulation of root development ...regulation of post-transcriptional gene silencing / : / L-pipecolic acid biosynthetic process / : / : / positive regulation of systemic acquired resistance / plant organ development / : / negative regulation of long-day photoperiodism, flowering / regulation of root development / negative regulation of flower development / regulation of root meristem growth / photoperiodism, flowering / plant-type hypersensitive response / positive regulation of defense response to bacterium / flower development / chromocenter / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K4 demethylase activity / plastid / negative regulation of gene expression, epigenetic / histone methyltransferase activity / developmental growth / histone demethylase activity / circadian rhythm / structural constituent of chromatin / nucleosome / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular region / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Yang, Z. / Du, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Plant Cell / Year: 2018 Title: Structure of the Arabidopsis JMJ14-H3K4me3 Complex Provides Insight into the Substrate Specificity of KDM5 Subfamily Histone Demethylases. Authors: Yang, Z. / Qiu, Q. / Chen, W. / Jia, B. / Chen, X. / Hu, H. / He, K. / Deng, X. / Li, S. / Tao, W.A. / Cao, X. / Du, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yko.cif.gz | 218.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yko.ent.gz | 171.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yko_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5yko_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5yko_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 5yko_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/5yko ftp://data.pdbj.org/pub/pdb/validation_reports/yk/5yko | HTTPS FTP |
-Related structure data
Related structure data | 5yknSC 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: 65001.832 Da / Num. of mol.: 1 / Mutation: E180A, E181A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: JMJ14, JMJ4, PKDM7B, At4g20400, F9F13.50 / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL References: UniProt: Q8GUI6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor | ||
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#2: Protein/peptide | Mass: 1192.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226 | ||
#3: Chemical | ChemComp-NI / | ||
#4: Chemical | #5: Chemical | ChemComp-OGA / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Na2SO4, 20% PEG 3350, 0.1M bis-tris propane, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 17462 / % possible obs: 99.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1702 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YKN Resolution: 2.9→39.338 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→39.338 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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