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Open data
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Basic information
Entry | Database: PDB / ID: 3hl2 | ||||||
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Title | The crystal structure of the human SepSecS-tRNASec complex | ||||||
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![]() | TRANSFERASE / selenocysteine / tRNASec / SepSecS / protein-RNA complex / Alternative splicing / Cytoplasm / Protein biosynthesis / Pyridoxal phosphate / Selenium | ||||||
Function / homology | ![]() O-phosphoseryl-tRNA(Sec) selenium transferase activity / O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase / conversion of seryl-tRNAsec to selenocys-tRNAsec / selenocysteine incorporation / Selenocysteine synthesis / tRNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Palioura, S. / Steitz, T.A. / Soll, D. / Simonovic, M. | ||||||
![]() | ![]() Title: The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation. Authors: Palioura, S. / Sherrer, R.L. / Steitz, T.A. / Soll, D. / Simonovic, 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 | ![]() | 437.2 KB | Display | ![]() |
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PDB format | ![]() | 356.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3bc8S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The physiologically active tetrameric assembly can be reconstructed by applying the following symmetry operation onto the chains A and B, and the conformer A of the chain E: X, X-Y, -Z (0 -1 0). Similarly, the physiologic tetramer can be built by applying the symmetry operation onto the chains C and D, and the conformer B of the chain E: -X+Y, Y, -Z+1/3 (0 0 0). |
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Components
-Protein / RNA chain , 2 types, 5 molecules ABCDE
#1: Protein | Mass: 55801.211 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9HD40, L-seryl-tRNASec selenium transferase #2: RNA chain | | Mass: 28908.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 299 molecules ![](data/chem/img/PLR.gif)
![](data/chem/img/TS6.gif)
![](data/chem/img/SEP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TS6.gif)
![](data/chem/img/SEP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PLR / ( #4: Chemical | #5: Chemical | ChemComp-SEP / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.33 % |
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Crystal grow | Temperature: 285 K / pH: 6.5 Details: 0.3M tri-lithium citrate, 18% (w/v) PEG 3,350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2008 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 89375 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 65.3 Å2 / Rsym value: 0.17 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1 / Rsym value: 0.94 / % possible all: 94.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BC8 Resolution: 2.81→37.95 Å / SU ML: 0.4 / 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: 48.94 Å2 / ksol: 0.28 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→37.95 Å
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LS refinement shell |
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