9RPL
Lactobacillus acidophilus SlpA self assembly domains I-II (aa 49-308)
Summary for 9RPL
| Entry DOI | 10.2210/pdb9rpl/pdb |
| Descriptor | S-layer protein, GLYCEROL, FORMIC ACID, ... (4 entities in total) |
| Functional Keywords | surface layer, self assembly, lactobacillus, structural protein |
| Biological source | Lactobacillus acidophilus NCFM |
| Total number of polymer chains | 2 |
| Total formula weight | 56323.44 |
| Authors | |
| Primary citation | Trivino, J.,Jimenez, E.,Grininger, C.,Caballero, I.,Medina, A.,Castellvi, A.,Petrillo, G.,Govantes, F.,Sagmeister, T.,Alcorlo, M.,Hermoso, J.A.,Sammito, M.D.,Diederichs, K.,Pavkov-Keller, T.,Uson, I. Guiding AlphaFold predictions with experimental knowledge to inform dynamics and interactions with VAIRO. Protein Sci., 35:e70481-e70481, 2026 Cited by PubMed Abstract: Structural predictions have reached unprecedented accuracy. They leverage sequence-specific data to capture all potential interactions a sequence has evolved to fulfill. AlphaFold derives information from three sources: learned parameters capturing intrinsic amino acid secondary structure and environment propensity; models of related proteins providing structural templates; and aligned sequences encoding profiles and concerted evolutionary changes of residues involved in contacts. However, function demands dynamic changes; hence not all possible interactions can coexist simultaneously. Comprehensive information entails contradictions, which resolved in favor of the better-informed structure will silence less stable states and associations. Here, we introduce a method using all three channels to include prior knowledge: site-specific variants, predefined alignments and templates. Selecting information relevant to a particular state delimits the functional context of a prediction. Our program VAIRO allows us to rescue asymmetric and weaker interactions to complete the view of molecular assemblies in the architecture of a bacterial surface layer, and reveals otherwise inaccessible dynamic states in a pneumococcal multimeric membrane protein complex. VAIRO is distributed via the python package index (PyPI) (https://pypi.org/project/vairo) and the code is also available on Github (https://github.com/arcimboldo-team/vairo). PubMed: 41578971DOI: 10.1002/pro.70481 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.93 Å) |
Structure validation
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