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Yorodumi- PDB-3k49: Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition seq... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k49 | ||||||
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Title | Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition sequence site B | ||||||
Components |
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Keywords | RNA Binding protein / RNA / PUF3 / PUMILIO / RNA BINDING / mitochondrial mRNA / Membrane / Mitochondrion / Mitochondrion outer membrane / Phosphoprotein / RNA-binding / RNA Binding protein - RNA COMPLEX | ||||||
Function / homology | Function and homology information regulation of ubiquinone biosynthetic process / cytoplasmic side of mitochondrial outer membrane / mitochondrion localization / intracellular mRNA localization / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / mitochondrion organization / mRNA 3'-UTR binding / positive regulation of translation / aerobic respiration ...regulation of ubiquinone biosynthetic process / cytoplasmic side of mitochondrial outer membrane / mitochondrion localization / intracellular mRNA localization / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / mitochondrion organization / mRNA 3'-UTR binding / positive regulation of translation / aerobic respiration / negative regulation of translation / mRNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zhu, D. / Stumpf, C.R. / Krahn, J.M. / Wickens, M. / Hall, T.M.T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs. Authors: Zhu, D. / Stumpf, C.R. / Krahn, J.M. / Wickens, M. / Hall, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k49.cif.gz | 245.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k49.ent.gz | 196.6 KB | Display | PDB format |
PDBx/mmJSON format | 3k49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k49_validation.pdf.gz | 500.4 KB | Display | wwPDB validaton report |
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Full document | 3k49_full_validation.pdf.gz | 524.6 KB | Display | |
Data in XML | 3k49_validation.xml.gz | 46.5 KB | Display | |
Data in CIF | 3k49_validation.cif.gz | 65.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/3k49 ftp://data.pdbj.org/pub/pdb/validation_reports/k4/3k49 | HTTPS FTP |
-Related structure data
Related structure data | 3k4eC 1m8yS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 42335.121 Da / Num. of mol.: 3 / Fragment: residues 511-879 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: L1325, PUF3, YLL013C / Plasmid: pTYB3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07807 #2: RNA chain | Mass: 3145.932 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: RNA oligonucleotides were obtained from Dharmacon, Inc. #3: Chemical | #4: 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: 2.7 Å3/Da / Density % sol: 54.47 % |
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Crystal grow | Temperature: 277 K / pH: 4.8 Details: 20% PEG4000, 0.1 M sodium citrate pH4.8, 2% dextran sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 26, 2007 |
Radiation | Monochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 48055 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.351 / % possible all: 83.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M8Y Resolution: 2.5→36.61 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 62.6 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→36.61 Å
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Refine LS restraints |
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LS refinement shell |
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