Task 4: Structural Alignments

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lab journal task 4

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.

Table 1: Table of the selected structures with their sequence identity to the refeerence 1A6Z_A.

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.

Table 2: Results of the structural alignments of the selected proteins to the template 1A6Z_A. The different alignment scores are listed for each method and the numbers of equivalen residues are stated in brackets after the RMSD.

PDB ID	Seq. identity (%)	Pymol		LGA		SSAP		TopMatch			CE
		RMSD (only C_alpha)	RMSD (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">

Table 3: Visualisation of the pariwise structural alignments of all selected proteins to the template 1A6Z_A. The template is shown in green and the target in red.

	1DE4_A	1QVO_A	1S7X_A	2IA1_A	3NCI_A	1VZY_A	1MUS_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