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- PDB-3mqk: Cbf5-Nop10-Gar1 complex binding with 17mer RNA containing ACA tri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mqk | ||||||
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Title | Cbf5-Nop10-Gar1 complex binding with 17mer RNA containing ACA trinucleotide | ||||||
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![]() | Isomerase/RNA binding protein/rna / Protein-RNA complex / Box H/ACA / pseudouridine synthase / post-transcriptional modification / Isomerase / tRNA processing / RNA-binding / Isomerase-RNA binding protein-rna complex | ||||||
Function / homology | ![]() tRNA pseudouridine(55) synthase activity / tRNA pseudouridine55 synthase / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / snRNA pseudouridine synthesis / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / positive regulation of telomerase RNA localization to Cajal body / telomerase RNA binding ...tRNA pseudouridine(55) synthase activity / tRNA pseudouridine55 synthase / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / snRNA pseudouridine synthesis / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / positive regulation of telomerase RNA localization to Cajal body / telomerase RNA binding / snoRNA binding / ribosome biogenesis / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, J. / Liang, B. / Li, H. | ||||||
![]() | ![]() Title: Structural and functional evidence of high specificity of Cbf5 for ACA trinucleotide. Authors: Zhou, J. / Liang, B. / Li, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.6 KB | Display | ![]() |
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PDB format | ![]() | 178.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ey4S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37119.305 Da / Num. of mol.: 1 / Fragment: UNP residues 8-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q7LWY0, Isomerases; Intramolecular transferases; Transferring other groups |
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#2: Protein | Mass: 6205.335 Da / Num. of mol.: 1 / Fragment: UNP residues 4-55 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 8672.303 Da / Num. of mol.: 1 / Fragment: UNP residues 8-82 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: RNA chain | Mass: 4117.501 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#5: RNA chain | Mass: 2814.759 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.14 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 120 mM magnesium acetate tetrahydrate, 50 mM MES PH 5.6, 20% 2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 19, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 20726 / % possible obs: 99.9 % / Redundancy: 20.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 48.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2000 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2EY4 Resolution: 2.8→33.378 Å / SU ML: 2.55 / σ(F): 0.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.496 Å2 / ksol: 0.307 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→33.378 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -12.2349 Å / Origin y: 35.566 Å / Origin z: -8.2205 Å
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Refinement TLS group | Selection details: all |