Structural Models
Secondary structure
The secondary structure of LL5β (human isoform a) has been predicted with Psipred, a server utilising position-specific scoring matrices [1][2].
The results are available here.
The secondary structure has also been predicted with Jpred4 [3][4][5][6].
Due to size restrictions, the sequence has been cleaved. Note that 9 amino-acid residues have been included in both sequences in order to analyse the secondary structure at the cleavage site.
The results can be downloaded here: part I and part II.
References
1. Buchan, D. W. A., Minneci, F., Nugent, T. C. O., Bryson, K., Jones, D. T. (2013) Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Research 41(W1):W340-W348.
2. Jones, D. T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 292:195-202.
3. Cole, C., Barber, J. D., Barton, G. J. (2008) The Jpred 3 secondary structure prediction server. Nucleic Acids Research 36(suppl. 2):W197-W201
4. Cuff, J. A., Barton, G. J. (2000) Application of Enhanced Multiple Sequence Alignment Profiles to Improve Protein Secondary Structure Prediction. PROTEINS: Structure, Function and Genetics 40:502-511
5. Cuff, J. A., Barton, G. J. (1999) Evaluation and Improvement of Multiple Sequence Methods for Protein Secondary Structure Prediction. PROTEINS: Structure, Function and Genetics 34:508-519
6. Cuff, J. A., Clamp, M. E., Siddiqui, A. S., Finlay, M. and Barton, G. J. (1998) Jpred: A Consensus Secondary Structure Prediction Server. Bioinformatics 14:892-893
7. Kelley, L. A., Sternberg, M. J. E. (2009) Protein structure prediction on the web: a case study using the Phyre server. Nature protocols 4:363-371
8. Källberg, M., Wang, H., Wang, S., Peng, J., Wang, Z., Lu, H., Xu, J. (2012) Template-based protein structure modeling using the RaptorX web server. Nature protocols 7:1511-1522
9. Ma, J., Wang, S., Zhao, F., Xu, J. (2013) Protein threading using context-specific alignment potential. Bioinformatics 29(13): i257-i265
10. Peng, J., Xu, J. (2011) A multiple-template approach to protein threading. Proteins 76(6):1930-1939
11. Peng, J., Xu, J. (2011) RaptorX: exploiting structure information for protein alignment by statistical inference. Proteins 79(S10): 161-171
12. The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
Tertiary structure
Phyre2, a protein modelling server using alignment to known protein structures [7] has been used to predict the tertiary structure of LL5β. 340 (27%) amino acid residues have been modelled with 99.7% confidence.
N-terminus is represented in blue and C-terminus in red.
The PDB file can be downloaded here.
A supplementary tertiary structure prediction has been obtained with RaptorX, a template-based modelling server [8][9][10][11].
607 amino-acid residues (48%) have been modelled, and 1099 residues (87%) have been predicted disordered.
The PDB file can be downloaded here.
The predicted structure has two domains. The small domain mainly composed of β-sheets has been predicted with a p-value of 9.65e-5. The large, mainly α- helical domain has a p-value of 1.17e-23.
Protein structures were rendered and animations created with PyMol [12].
