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Yorodumi- PDB-3vnb: Structural insights into small RNA sorting and mRNA binding by Ar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vnb | ||||||
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Title | Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago domains | ||||||
Components | Protein argonaute 1 | ||||||
Keywords | RNA BINDING PROTEIN / Rossmann fold / 5'-end nucleotide binding | ||||||
Function / homology | Function and homology information adaxial/abaxial pattern specification / adventitious root development / auxin metabolic process / leaf morphogenesis / leaf proximal/distal pattern formation / RNAi-mediated antiviral immune response / leaf vascular tissue pattern formation / response to far red light / post-transcriptional gene silencing / response to auxin ...adaxial/abaxial pattern specification / adventitious root development / auxin metabolic process / leaf morphogenesis / leaf proximal/distal pattern formation / RNAi-mediated antiviral immune response / leaf vascular tissue pattern formation / response to far red light / post-transcriptional gene silencing / response to auxin / miRNA-mediated post-transcriptional gene silencing / siRNA binding / miRNA binding / RNA endonuclease activity / regulation of translation / defense response to virus / cell differentiation / ribonucleoprotein complex / mRNA binding / innate immune response / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Yuan, Y.A. / Zha, X. | ||||||
Citation | Journal: Febs Lett. / Year: 2012 Title: Structural insights into small RNA sorting and mRNA target binding by Arabidopsis Argonaute Mid domains Authors: Zha, X. / Xia, Q. / Yuan, Y.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vnb.cif.gz | 73.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vnb.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 3vnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/3vnb ftp://data.pdbj.org/pub/pdb/validation_reports/vn/3vnb | HTTPS FTP |
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-Related 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: 17613.582 Da / Num. of mol.: 1 / Fragment: Mid domain, UNP residues 592-739 / Mutation: INSERTION AND MUTATIONS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: O04379 | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Ammonium sulfate, citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 23600 / Num. obs: 23590 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Rsym value: 0.069 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 13.7 % / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→45.18 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.481 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.822 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→45.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.502→1.541 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0.7671 Å / Origin y: 4.4264 Å / Origin z: 9.6235 Å
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