[English] 日本語
Yorodumi- PDB-7o6t: Crystal structure of the polymerising VEL domain of VIN3 (R556D I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o6t | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the polymerising VEL domain of VIN3 (R556D I575D mutant) | |||||||||
Components | (Protein VERNALIZATION INSENSITIVE 3) x 2 | |||||||||
Keywords | NUCLEAR PROTEIN / protein oligomerization / head-to-tail polymerization / domain swapping | |||||||||
Function / homology | Function and homology information vernalization response / chromatin silencing complex / cellular response to cold / negative regulation of gene expression, epigenetic / response to cold / response to hypoxia / nuclear speck / DNA binding / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å | |||||||||
Authors | Fiedler, M. / Franco-Echevarria, E. / Dean, C. / Bienz, M. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: Cell Rep / Year: 2022 Title: Head-to-tail polymerization by VEL proteins underpins cold-induced Polycomb silencing in flowering control. Authors: Fiedler, M. / Franco-Echevarria, E. / Schulten, A. / Nielsen, M. / Rutherford, T.J. / Yeates, A. / Ahsan, B. / Dean, C. / Bienz, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7o6t.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7o6t.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 7o6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/7o6t ftp://data.pdbj.org/pub/pdb/validation_reports/o6/7o6t | HTTPS FTP |
---|
-Related structure data
Related structure data | 7o6uC 7o6vC 7o6wC 7oqvC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8725.775 Da / Num. of mol.: 1 / Mutation: R556D I575D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VIN3, At5g57380, MSF19.4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FIE3 |
---|---|
#2: Protein | Mass: 8649.657 Da / Num. of mol.: 1 / Mutation: R556D I575D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VIN3, At5g57380, MSF19.4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FIE3 |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.33 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.06M Morpheus Divalents, 0.1M Morpheus Buffer System 2 pH 7.5, 10% w/v PEG 8K, 20% v/v ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→29.49 Å / Num. obs: 9677 / % possible obs: 99.7 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 36.2 |
Reflection shell | Resolution: 2.02→2.07 Å / Num. unique obs: 677 / CC1/2: 0.93 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.02→29.49 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 11.826 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.648 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→29.49 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.02→2.069 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|