Round 47

Registration is closed Participant list

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Announcement

The protein is the assembly domain of SAP (Uniprot: P49051) the surface layer (S-layer) protein from Bacillus anthracis.  This assembly domain, comprises residues 216-814 of the full SAP protein and folds into 6 discrete structural domains (D1-D6). These domains self assemble into a 2D array whose structure is currently under study by Cryo-EM.

The 3D structure of the isolated SAP assembly domain in complex with two (different) nanobodies was solved to high resolution by X-ray diffraction (2 different crystal forms, displaying the same 3D fold of the SAP domain have been determined), and is being offered to CAPRI by Han Remaut and Antonella Floravanti from the VIB-VUB Center for Structural biology, in Brussels, Belgium.

The information provided to predictors is: the sequences of the SAP assembly domain (residues 216-814), and the two nanobodies Nb684 and Nb694.

To facilitate the task of modeling the SAP 3D structure, we also provide the atomic coordinates of the backbone atoms of individual domains (D1-D6) in random orientation and translation.

This prediction challenge consists of modeling the 3D structure of the SAP assembly domain e.g. the intra-molecular contacts between the SAP domains, as well as the conformations of the connecting loops, as well as the complex with the 2 nanobodies.

We will evaluate separately the predicted 3D structure of the protein (e.g. intra- domain-domain interactions in particular) and the structure of the complexes (interfaces & contacts) with the 2 nanobodies. Given the difficulty of integrating the 3D structure and complex predictions, the deadlines for the server and predictor submissions will be extended (see timelines).

We were unfortunately unable to break down this target into 2 independent prediction problems (1^st the 3D structure of the SAP assembly domain, 2^nd its complex with the nanobodies), given the tight publication schedule of the authors.

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Targets

Dates

Registration starts: Jan. 22, 2019

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