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- PDB-3oin: Crystal structure of Saccharomyces cerevisiae Nep1/Emg1 bound to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3oin | |||||||||
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Title | Crystal structure of Saccharomyces cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA | |||||||||
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![]() | RIBOSOMAL PROTEIN / EMG1 / scNEP1 / SPOUT / ribosome biogenesis / methyltransferase / rRNA processing | |||||||||
Function / homology | ![]() rRNA small subunit pseudouridine methyltransferase Nep1 / nuclear microtubule / rRNA (pseudouridine) methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA base methylation / rRNA methylation / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...rRNA small subunit pseudouridine methyltransferase Nep1 / nuclear microtubule / rRNA (pseudouridine) methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA base methylation / rRNA methylation / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / rRNA binding / nucleolus / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Thomas, S.R. / LaRonde-LeBlanc, N. | |||||||||
![]() | ![]() Title: Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis. Authors: Thomas, S.R. / Keller, C.A. / Szyk, A. / Cannon, J.R. / Laronde-Leblanc, N.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.9 KB | Display | ![]() |
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PDB format | ![]() | 164.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3o7bC ![]() 3oiiC ![]() 3oijC ![]() 2v3jS C: citing same article ( 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
-Protein / RNA chain , 2 types, 3 molecules ABC
#1: Protein | Mass: 28035.549 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: EMG1, NEP1, YLR186W, L9470.5 / Plasmid: pDest527 / Production host: ![]() ![]() References: UniProt: Q06287, rRNA small subunit pseudouridine methyltransferase Nep1 #2: RNA chain | | Mass: 4437.699 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Cognate RNA synthesized to mimic natural RNA substrate Source: (synth.) ![]() ![]() |
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-Non-polymers , 5 types, 246 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-SAH / | #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES, 10% PEG 6000, 20% glycerol, pH 7.0, Vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00931 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→30 Å / Num. all: 37461 / Num. obs: 36263 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Χ2: 0.928 / Net I/σ(I): 25.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2V3J Resolution: 1.9→27.68 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8151 / SU ML: 0.21 / σ(F): 1.34 / 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: 59.156 Å2 / ksol: 0.339 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 181.36 Å2 / Biso mean: 48.1209 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→27.68 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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