Task 4: Structural Alignments
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PDB structures selection
We first selected a set of structures that span different ranges of sequence identity to the reference structure (1A6Z,A). The reference structure has the CATH numbers 3.30.500.10.9 (Murine Class I Major Histocompatibility Complex H2-DB subunit A domain 1) and also 2.60.40.10 (immunoglobulins). We decided to search for structures with a similar annotation to 3.30.500.10.9, since the immunglobulin domain is only bound to the protein. Also, because the disease causing mutations are all located in the MHC domain. Table ??? list the structures, their CATH numbers and percent sequence iden Edittity to the reference. Unfortunately, we could not find a structure with a sequence identity over 60%. The most similar structure we could find was 1qvo with 39% identity.
| category | ID | chain | domain | CATH number | Sequence identity (%) |
|---|---|---|---|---|---|
| reference | 1a6z | A | 1 | 3.30.500.10 | |
| identical sequence | 1de4 | A | 1 | 3.30.500.10 | 100 |
| > 30% SeqID | 1qvo | A | 01 | 3.30.500.10 | 39 |
| < 30% SeqID | 1S7X | A | 00 | 3.30.500.10 | 29 |
| CAT | 2ia1 | A | 01 | 3.30.500.20 | 11.1 |
| CA | 3nci | A | 01 | 3.30.342.10 | 5.8 |
| C | 1vzy | A | 01 | 3.55.30.10 | 2.8 |
| different CATH | 1mus | A | 01 | 1.10.246.40 | 12.6 |
The pairwise sequence alignments for computing the pairwise sequence identity were constructed with Emboss Needle http://www.ebi.ac.uk/Tools/psa/emboss_needle/ using default parameters.
Results
Differenct structural alignments were applied to superimpose the reference structure to all other structures. The resulting alignments scores are specified in table ????. The numbers in bracket after the RMSD values indicate the number of aligned residues that were used to compute the corresponding value.
| PDB id | Seq. identity (%) | Pymol (RMSD) | LGA | SSAP | TopMatch | CE | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| only C_alpha | all atom | RMSD | LGA_S | RMSD | SSAP_Score | RMSD | S | S_r | RMSD | Score | ||
| 1DE4_A | 100 | 0.675 (237) | 0.767 (1836) | 1.14 (267) | 95.77 | 1.60 (272) | 93.07 | 1.08 | 260 | 1.03 | 1.19 (267) | 543 |
| 1QVO_A | 39 | 2.165 (233) | 2.279 (1565) | 2.29 (259) | 67.86 | 2.58 (268) | 86.39 | 2.62 | 228 | 2.50 | 2.44 (266) | 432 |
| 1S7X_A | 29 | 1.889 (233) | 2.049 (1557) | 2.12 (256) | 71.90 | 2.36 (267) | 86.25 | 2.66 | 227 | 2.56 | 2.29 (265) | 342 |
| 2IA1_A | 11.1 | 18.132 (74) | 18.283 (501) | 2.83 (86) | 19.44 | 15.85 (140) | 56.19 | 2.91 | 76 | 2.82 | 3.93 (93) | 300 |
| 3NCI_A | 5.8 | 16.561 (26) | 17.329 (178) | 3.11 (84) | 17.19 | 14.54 (168) | 30.18 | 3.05 | 53 | 2.94 | 4.47 (75) | 333 |
| 1VZY_A | 2.8 | 6.260 (29) | 6.951 (168) | 3.25 (63) | 13.44 | 26.34 (208) | 58.01 | 2.61 | 68 | 2.53 | 5.80 (91) | 245 |
| 1MUS_A | 12.6 | 23.521 (180) | 23.891 (1143) | 2.82 (69) | 16.02 | 18.53 (215) | 46.30 | 3.58 | 69 | 3.43 | 6.61 (78) | 379 |
<figtable id="Structural alignments with Pymol to 1A6Z_A">
| 1DE4_A |
</figtable>
- Pymol only uses a subset of atoms for the computation of the RMSD.
- LGA computes the RMSD from all atoms under distance cutoff. It therfore uses more atoms than Pymol if the proteins are similar, but few if the structures are more divergent.
- SSAP
- TopMatch
- CE
