| Target: R1260 |
| Target: |
R1260 |
| Type: |
All-group target
|
| Is protein multimer? |
No
|
| Is CAPRI target? |
No |
| Is ligand target? |
No
|
| Entry Date: |
2024-06-07 |
| Server Expiration Date: |
2024-08-06 |
| Human Expiration Date: |
2024-08-06 |
|
| Protein: |
Ribozyme solvent shell |
| Organism: |
tetrahymena |
| Residues: |
387 |
| Method: |
EM
|
| Additional Information: |
Predictors are invited to submit an ensemble of conformations of this RNA with the solvent shell. The structure of the local solvent shell (water and ions) will be compared against cryo-EM data.
We provide the following experimental information. These samples were folded and frozen in a solution of 50 mM Na-HEPES pH 8.0 and 10 mM MgCl2. The sample was folded for 30 min at 50°C, incubated at room temperature for 10 min, and then placed on ice. The sample was frozen on Vitrobot Mark IV with 4 s blot time, 4°C, and 100% humidity using liquid ethane as cryogen. A total electron dose of 57.25 electrons per Angstrom squared was used during data collection. The cryo-EM maps are 2.2 and 2.3 Angstrom according to gold standard FSC and were auto-sharpened using PHENIX.
We require, for each conformation, that the RNA coordinates be present and that you submit at least a 5 Angstrom shell of water and ions. Larger solvent shells are allowed but may not be assessed. The RNA conformation may change across the frames. The RNA motion will not be assessed but the predictors are welcome to submit RNA of different conformations. Predictors can assume that the RNA conformations are similar to 7EZ0 (eg. <4 Angstrom RMSD). During assessment these models will be locally aligned before comparing solvent structure. The main assessment will be on the local water and ion structure surrounding each RNA region, based on local alignments compared to experimentally determined high-resolution maps. Given experimental uncertainty in some regions, the solvent structure around the following residues will not be assessed: 42-67, 208-224, 263-274, 311-314, 343-381 (7EZ0 numbering: 63-88, 229-245, 284-295, 332-335, 364-402).
To reduce file size, please remove all hydrogen atoms. Please submit as a set of PDB files, these should be tarred, gzipped, and uploaded as one archive file through https://predictioncenter.org/casp16/predictions_submission_WATER.cgi. To create an archive, please run: tar -czf R1260TS234.tgz ./Folder_with_R1260_models. Archive file names should combine the target name R1260 and the group name (234 in the provided example). Names of individual models inside the archive should follow the CASP model naming scheme, e.g. R1260TS234_1, where _1 is the model number. You may submit up to 1,000 conformations, with a suggested minimum of 10. We will assume equal weighting of all models in the ensemble; you may repeat conformations in the ensemble if you wish to give those conformations greater weight. |
Sequence: (Plain text version)
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Template: (Plain text version)
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