Targets - CASP13

Sequence Name:	T0979
Target:
Sequence(s):	>A0A0G1XU35_9BACT-fragment-between-GCN4-adaptors GGGSGMKQLEDKVEELLSKVYHLENEVARLKKLFAETATKAETATKAETATKKDIAGMATKHDIAQLDKRMKQLEWKVEELLSKVYHLENEVARLKKL
Comments:	This is the first oligomeric refinement target in CASP. Being a trimer, it is somewhat longer than other refinement targets in CASP13: 276 residues total. GDT_HA of the starting model's monomeric unit is 55 (on 92 residues; residues 1-5 and 98 are absent from the experimental structure). LDDT score of the oligomeric starting model is 0.81; the inter-chain contact accuracy score F1=43%. All rules pertaining to submission of regular homo-oligomeric targets apply here.
Subunit(s):	1
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Sequence summary:	Sequence TSID: 85 Target: T0979 SEQUENCE : >A0A0G1XU35_9BACT-fragment-between-GCN4-adaptors GGGSGMKQLEDKVEELLSKVYHLENEVARLKKLFAETATKAETATKAETATKKDIAGMATKHDIAQLDKRMKQLEWKVEELLSKVYHLENEVARLKKL NUMBER_OF_AA : 98 REAL_NUMBER_OF_AA : 98 SGI_CENTER : Others OLIGOMERIC_STATE : trimeric BINDING_SITES : n/a LIGANDS : n/a STOICHIOMETRY : A3 DISORDER : 1-5 SOLVENT : Protein buffer: 20mM Tris pH 7.6, 150mM NaCl; Cysallization buffer: 0.1M Na.acetate pH 4.6, 2M Na.formate PROTEIN_MATERIAL : NO EXPRESSION : Bacterial BLAST_INFO : HHSEARCH_INFO : DIFFICULTY : Other info : We predicted the sequence to form a yet unobserved fiber structure. It was fused N- and C-terminally to GCN4 adaptors for stabilization. It is a homo trimeric fiber. This is the sequence of the construct: GGGSG-MKQLEDKVEELLSKVYHLENEVARLKKL-FAETATKAETATKAETATKKDIAGMATKHDIAQLDKR-MKQLEWKVEELLSKVYHLENEVARLKKL The part of interest is the sequence FAETATKAETATKAETATKKDIAGMATKHDIAQLDKR in the middle. It is from a hypothetical protein from an uncharacterized Parcubacterium: _ KKW34673.1 hypothetical protein UY81_C0065G0003 _Candidatus Giovannonibacteria bacterium GW2011_GWA2_53_7_ MKKPITLEKLVSMVAVGFAETATKAETATKAETATKKDIAGMATKHDIAQLDKRIDGLDKKIADLVDRIGRVESKLDRALNKEVAAWKVSSAS We have no idea what it does, but we thought it should form a trimeric fiber of a type that we call a alpha_beta coiled coil. We previously characterized alpha_beta coiled coils with a sequence repeat length of 9 residues (http:__dx.doi.org_10.7554_eLife.11861.001 or PDB:5APZ). Now this one has repeats of 6 residues, such that it is almost a clean beta-only coiled coil without real alpha content. I could anticipate that manual predictors could have a good chance of cracking it, while automated servers should rather fail. The structure I appended has the sequence of interest fused to stabilizing GCN4 leucine zipper domains. The quality of the crystallographic model is not fully satisfactory yet, including parts of the backbone geometry in the region of interest. However, we are actively working on the structure solution and refinement of other crystal forms at higher resolution, so we probably could provide a better model soon.