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- PDB-3k4e: Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition seq... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k4e | ||||||
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Title | Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition sequence site A | ||||||
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![]() | 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 | ![]() regulation of ubiquinone biosynthetic process / mitochondrion localization / cytoplasmic side of mitochondrial outer membrane / intracellular mRNA localization / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / aerobic respiration / mitochondrion organization / mRNA 3'-UTR binding / positive regulation of translation ...regulation of ubiquinone biosynthetic process / mitochondrion localization / cytoplasmic side of mitochondrial outer membrane / intracellular mRNA localization / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / aerobic respiration / mitochondrion organization / mRNA 3'-UTR binding / positive regulation of translation / negative regulation of translation / mRNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhu, D. / Stumpf, C.R. / Krahn, J.M. / Wickens, M. / Hall, T.M.T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.5 KB | Display | ![]() |
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PDB format | ![]() | 184.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 482.5 KB | Display | ![]() |
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Full document | ![]() | 489.2 KB | Display | |
Data in XML | ![]() | 36.8 KB | Display | |
Data in CIF | ![]() | 51.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3k49SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() Strain: genomic DNA / Gene: L1325, PUF3, YLL013C / Plasmid: pTYB3 / Production host: ![]() ![]() #2: RNA chain | Mass: 3123.876 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: RNA oligonucleotides were obtained from Dharmacon, Inc References: ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.21 % |
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Crystal grow | Temperature: 277 K / pH: 4.8 Details: 20% PEG4000, 0.1 M sodium citrate pH 4.8, 2% dextran sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 12, 2008 |
Radiation | Monochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 23487 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.453 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3K49 Resolution: 3.2→28.91 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 63 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→28.91 Å
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Refine LS restraints |
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LS refinement shell |
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