2AQ3: T-cell receptor V beta domain variant

Crystal structure of T-cell receptor V beta domain variant complexed with superantigen SEC3. Determined by X-ray diffraction at 2.3 Å resolution. Released 21 Mar 2006.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Mus musculus, Staphylococcus aureus
Chains: 8
Atoms: 11,155
Mol. weight: 158.12 kDa
Released: 21 Mar 2006

Explore 2AQ3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2AQ3 contains 35 α-helices and 121 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-21	3	3
β-strand	22-25	4	1
β-strand	31-38	8	2
β-strand	41-49	9	2
β-strand	56-57	2	2
β-strand	65-68	4	3
β-strand	74	1	1
β-strand	76-79	4	3
α-helix	84-86	3
β-strand	88-91	4	2
β-strand	93-96	4	2
β-strand	99-108	4	2
β-strand	112-116	5	2

Chain B: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
β-strand	17	1	4
α-helix	22-28	7
β-strand	35-39	5	5
β-strand	42	1	6
β-strand	48-52	5	6
β-strand	63-67	5	6
α-helix	71-78	8
β-strand	81-84	4	5
β-strand	89	1	6
β-strand	106-110	5	6
β-strand	114-115	2	5
β-strand	120	1	7
β-strand	127-135	9	8
β-strand	139-147	9	8
β-strand	149	1	7
β-strand	151-152	2	9
α-helix	154-168	15
β-strand	179-187	9	8
β-strand	193-197	5	8
β-strand	203	1	4
α-helix	208-211	4
α-helix	212-215	4
β-strand	221-222	2	9
α-helix	223-225	3
β-strand	227-234	8	8

Chain C: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	10
β-strand	10-13	4	11
β-strand	19-21	3	12
β-strand	24	1	10
β-strand	32-37	6	11
β-strand	44-49	6	11
β-strand	56-57	2	11
β-strand	65-68	4	12
β-strand	76-79	4	12
α-helix	84-86	3
β-strand	88-94	7	11
β-strand	95	1	13
β-strand	100	1	13
β-strand	112-116	5	11

Chain D: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	14-16	3
β-strand	17	1	14
α-helix	22-28	7
β-strand	33-38	6	15
β-strand	42	1	16
β-strand	48-51	4	16
β-strand	63-67	5	16
α-helix	71-77	7
β-strand	82-86	5	15
β-strand	89	1	16
β-strand	106-110	5	16
β-strand	113-115	3	15
β-strand	128-135	8	17
β-strand	138-146	9	17
β-strand	151-153	3	18
α-helix	154-167	14
β-strand	181-187	7	17
β-strand	193-197	5	17
α-helix	200-201	2
β-strand	203	1	14
α-helix	208-211	4
α-helix	212-217	6
β-strand	220-222	3	18
β-strand	227-233	7	17

Chain E: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	5	1
β-strand	6-7	2	19
β-strand	12-13	2	20
β-strand	19-24	6	19
β-strand	32-38	7	21
β-strand	42-49	8	21
β-strand	56-57	2	21
β-strand	65-68	4	19
β-strand	74-79	6	19
α-helix	84-86	3
β-strand	88-94	7	21
β-strand	100	1	13
β-strand	112-114	3	21
β-strand	115-116	2	20

Chain F: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14-16	3
β-strand	17	1	22
α-helix	22-25	4
β-strand	33-38	6	23
β-strand	42	1	24
β-strand	48-51	4	24
β-strand	64-67	4	24
α-helix	71-77	7
β-strand	82-86	5	23
β-strand	89	1	24
β-strand	107-110	4	24
β-strand	113-115	3	23
β-strand	127-135	9	25
β-strand	138-147	10	25
β-strand	151-153	3	26
α-helix	154-169	16
β-strand	179-187	9	25
β-strand	195-197	3	25
α-helix	200-201	2
β-strand	203	1	22
α-helix	212-215	4
β-strand	220-222	3	26
β-strand	227-234	8	25

Chain G: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	27
β-strand	10-13	4	2
β-strand	19-25	7	27
β-strand	31-38	8	2
β-strand	42-49	8	2
β-strand	56-57	2	2
β-strand	65-68	4	27
β-strand	74-79	6	27
α-helix	84-86	3
β-strand	88-96	9	2
β-strand	99-108	4	2
β-strand	112-116	5	2

Chain H: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	13	1	28
β-strand	17	1	29
α-helix	22-28	7
β-strand	33-38	6	30
β-strand	42	1	31
β-strand	48-51	4	31
β-strand	64-67	4	31
α-helix	71-77	7
β-strand	82-86	5	30
β-strand	88-89	2	31
β-strand	107-109	3	31
β-strand	113-115	3	30
α-helix	125-126	2
β-strand	127-135	9	28
β-strand	138-147	10	28
β-strand	151-153	3	32
α-helix	154-169	16
β-strand	181-187	7	28
β-strand	193-197	5	28
α-helix	200-201	2
β-strand	203	1	29
α-helix	208-212	5
α-helix	213-215	3
β-strand	220-222	3	32
β-strand	227-233	7	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell receptor beta chain V	A, C, E, G	protein	112	Mus musculus	P04213 (AlphaFold model)
Enterotoxin type C-3	B, D, F, H	protein	237	Staphylococcus aureus	P0A0L5 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>2AQ3_1 T-cell receptor beta chain V (chains A, C, E, G)
ILEAAVTQSPRNKVAVTGEKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKG
DIPDGYKASRPSQEQFSLILESATPSQTSVYFCASGGGGTLYFGAGTRLSVL

Sequence of entity 2 (B, D, F, H), FASTA

>2AQ3_2 Enterotoxin type C-3 (chains B, D, F, H)
ESQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKN
YDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFSSKDGKVTGGKTCMYGGITKHEGNH
FDNGNLQNVLVRVYENKRNTISFEVQTDKKSVTAQELDIKARNFLINKKNLYEFNSSPYE
TGYIKFIENNGNTFWYDMMPAPGDKFDQSKYLMMYNDNKTVDSKSVKIEVHLTTKNG

Primary citation

Structural basis of affinity maturation and intramolecular cooperativity in a protein-protein interaction. Cho, S., Swaminathan, C.P., Yang, J. et al. Structure (2005) 13:1775-1787. DOI 10.1016/j.str.2005.08.015 · PubMed

Other PDB entries of the same protein (UniProt P04213 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5M02 1.75 Å, Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
2APB 1.8 Å, Crystal Structure of the S54N variant of murine T cell receptor Vbeta 8.2 domain
2APF 1.8 Å, Crystal Structure of the A52V/S54N/K66E variant of the murine T cell receptor V beta 8.2…
2APX 1.8 Å, Crystal Structure of the G17E/A52V/S54N/K66E/Q72H/E80V/L81S/T87S/G96V variant of the…
2AQ2 1.8 Å, Crystal structure of T-cell receptor V beta domain variant complexed with superantigen…
6G9Q 1.89 Å, Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen…
2APV 1.9 Å, Crystal Structure of the G17E/A52V/S54N/Q72H/E80V/L81S/T87S/G96V variant of the murine T…
5M00 1.95 Å, Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide…
5M01 1.95 Å, Crystal structure of murine P14 TCR/ H-2Db complex with PA, modified gp33 peptide from…
1LP9 2.0 Å, Xenoreactive complex AHIII 12.2 TCR bound to p1049/HLA-A2.1
2APT 2.0 Å, Crystal Structure of the G17E/S54N/K66E/Q72H/E80V/L81S/T87S/G96V variant of the murine T…
2APW 2.0 Å, Crystal Structure of the G17E/A52V/S54N/K66E/E80V/L81S/T87S/G96V variant of the murine T…

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