| Target: E2460 |
| Target: |
E2460 |
| Type: |
All-group target
|
| Entry Date: |
2026-07-30 |
| Server Expiration Date: |
2026-08-06 |
| Human Expiration Date: |
2026-08-31 |
|
| Protein: |
CBM56 |
| Organism: |
Nialla circulans |
| Residues: |
205 |
| Method: |
X-RAY
|
| Additional Information: |
This is a Domain-Linker-Domain target, in which the goal is to model the conformational distribution of the two domains with respect to each other. These distributions will be assessed against both FRET and SAXS data. The proposed target is Carbohydrate-Binding Module Family 56 (CBM56), described below. A set of 27 variants with FRET pairs at distinct positions were used to generate ground truth data for 27 interdye distances distributions (mean and width) with nanosecond time resolution by time-resolved single-molecule FRET spectroscopy with multiparameter detection. The dyes were placed on flexible regions (loops) and rigid regions (beta sheet) of the domains. We found a consistently broadened FRET population whose interdye distances are significantly broader than that of a single state. We applied fluorescence correlation spectroscopy to probe the conformational flexibility of CBM56. Depending on the labeling position, we found relaxation times ranging from 100 ns to 1 ms. This kinetic analysis indicates conformational flexibility and supports the finding of conformational heterogeneity above.
At this point, we are not satisfied with the available SAXS data. Accordingly, this target will be posted in the CASP Prediction Target list, with instructions for submission of ensemble predictions. However, we will not be certain until early fall if a proper assessment can be made. We will inform you as soon as possible when improved SAXS data will be available for assessment.
Please model "ensembles" of conformational states for the provided protein sequence. You may submit up to 1000 all-atom conformer models that include all residues specified in the sequence; incomplete models will not be evaluated. The coordinate models should be supplemented by a populations.txt file listing each model of the ensemble with the corresponding relative population, expressed as a positive rational number. The sum of all populations should equal 1.0. All conformational ensembles are to be submitted through the dedicated CASP17 gateway https://predictioncenter.org/casp17/predictions_submission_ENSMBL.cgi, which provides further instructions on preparing submissions.
Predictors should include a comment on why they chose a certain number of conformers. If possible, the predictors should also provide information on the flexibility/rigidity between but also within the two domains. |
Sequence: (Plain text version)
|
Template: (Plain text version)
|
