3BYT: T cell receptor beta chain 8.2

Name: PDB 3BYT: A complex between a variant of staphylococcal enterotoxin C3 and the variable domain of the murine T cell receptor beta chain 8.2
Published: 2009-05-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

A complex between a variant of staphylococcal enterotoxin C3 and the variable domain of the murine T cell receptor beta chain 8.2. Determined by X-ray diffraction at 2.3 Å resolution. Released 12 May 2009.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Mus musculus, Staphylococcus aureus
Chains: 8
Atoms: 11,054
Mol. weight: 158.24 kDa
Released: 12 May 2009

Explore 3BYT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3BYT contains 37 α-helices and 125 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, 13 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	31-37	7	2
β-strand	44-49	6	2
β-strand	56-57	2	2
β-strand	64-67	4	3
β-strand	73	1	1
β-strand	75-78	4	3
α-helix	83-85	3
β-strand	87-94	8	2
β-strand	98-101	4	2
β-strand	105-109	5	2

Chain B: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	12-13	2
α-helix	14-16	3
β-strand	17	1	4
α-helix	22-28	7
β-strand	33-38	6	5
β-strand	42	1	6
β-strand	48-51	4	6
β-strand	63-67	5	6
α-helix	71-78	8
β-strand	82-86	5	5
β-strand	89	1	6
β-strand	106-110	5	6
β-strand	113-115	3	5
β-strand	120	1	7
β-strand	127-135	9	8
β-strand	138-147	10	8
β-strand	149	1	7
β-strand	151-153	3	9
α-helix	154-169	16
β-strand	181-187	7	8
β-strand	193-197	5	8
α-helix	200-201	2
β-strand	203	1	4
α-helix	208-211	4
α-helix	212-217	6
β-strand	220-222	3	9
β-strand	227-233	7	8

Chain C: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-13	4	11
β-strand	19-21	3	12
β-strand	22-25	4	10
β-strand	31-37	7	11
β-strand	43-49	7	11
β-strand	56-57	2	11
β-strand	65-68	4	12
β-strand	74	1	10
β-strand	76-79	4	12
α-helix	84-86	3
β-strand	88-95	8	11
β-strand	99-101	3	11
β-strand	112-116	5	11

Chain D: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	14-16	3
β-strand	17	1	13
α-helix	22-28	7
β-strand	33-38	6	14
β-strand	42	1	15
β-strand	48-51	4	15
β-strand	63-67	5	15
α-helix	71-77	7
β-strand	82-86	5	14
β-strand	89	1	15
β-strand	106-110	5	15
β-strand	113-115	3	14
β-strand	120	1	16
β-strand	127-135	9	17
β-strand	139-147	9	17
β-strand	149	1	16
β-strand	151-153	3	18
α-helix	154-169	16
β-strand	179-187	9	17
β-strand	193-197	5	17
β-strand	203	1	13
α-helix	208-211	4
α-helix	212-217	6
β-strand	220-222	3	18
β-strand	227-234	8	17

Chain E: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-13	4	11
β-strand	19-25	7	19
β-strand	31-37	7	11
β-strand	43-49	7	11
β-strand	57	1	11
β-strand	65-71	7	19
β-strand	74-79	6	19
α-helix	84-86	3
β-strand	88-95	8	11
β-strand	99-108	4	11
β-strand	112-116	5	11

Chain F: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	17	1	20
α-helix	22-28	7
β-strand	33-38	6	21
β-strand	42	1	22
β-strand	48-51	4	22
β-strand	64-67	4	22
α-helix	71-77	7
β-strand	82-86	5	21
β-strand	89	1	22
β-strand	107-110	4	22
β-strand	113-115	3	21
β-strand	120	1	23
β-strand	127-135	9	24
β-strand	139-147	9	24
β-strand	149	1	23
β-strand	151-153	3	25
α-helix	154-169	16
β-strand	181-187	7	24
β-strand	193-197	5	24
α-helix	200-201	2
β-strand	203	1	20
α-helix	208-212	5
α-helix	213-217	5
β-strand	220-222	3	25
β-strand	227-233	7	24

Chain G: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	26
β-strand	10-13	4	2
β-strand	19-21	3	27
β-strand	22-25	4	26
β-strand	31-37	7	2
β-strand	43-49	7	2
β-strand	56-57	2	2
β-strand	65-68	4	27
β-strand	76-79	4	27
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	99-108	4	2
β-strand	112-116	5	2

Chain H: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	8-10	3
α-helix	12-13	2
α-helix	14-16	3
β-strand	17	1	28
α-helix	22-25	4
β-strand	33-38	6	29
β-strand	42	1	30
β-strand	48-51	4	30
β-strand	63-67	5	30
α-helix	71-77	7
β-strand	82-86	5	29
β-strand	89	1	30
β-strand	106-110	5	30
β-strand	113-115	3	29
β-strand	120	1	31
β-strand	127-135	9	32
β-strand	138-147	10	32
β-strand	149	1	31
β-strand	151-153	3	33
α-helix	154-169	16
β-strand	181-187	7	32
β-strand	193-197	5	32
α-helix	200-201	2
β-strand	203	1	28
α-helix	208-212	5
α-helix	213-215	3
β-strand	220-222	3	33
β-strand	227-233	7	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T cell receptor beta chain 8.2	A, C, E, G	protein	109	Mus musculus
Enterotoxin type C-3	B, D, F, H	protein	239	Staphylococcus aureus	P0A0L5 (AlphaFold model)

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

>3BYT_1 T cell receptor beta chain 8.2 (chains A, C, E, G)
AAVTQSPRNKVAVTGEKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIP
DGYKASRPSQEQFSLILESATPSQTSVYFCASGGGGTLYFGAGTRLSVL

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

>3BYT_2 Enterotoxin type C-3 (chains B, D, F, H)
ESQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKN
YDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFSSKDNKASTWHGKTCMYGGITKHEG
NHFDNGNLQNVLVRVYENKRNTISFEVQTDKKSVTAQELDIKARNFLINKKNLYEFNSSP
YETGYIKFIENNGNTFWYDMMPAPGDKFDQSKYLMMYNDNKTVDSKSVKIEVHLTTKNG

Primary citation

Manipulating the coupled folding and binding process drives affinity maturation in a protein-protein complex. Cho, S., Swaminathan, C.P., Kerzic, M.C. et al. To be published.

Other PDB entries of the same protein (UniProt P0A0L5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2AQ2 1.8 Å, Crystal structure of T-cell receptor V beta domain variant complexed with superantigen…
1KLU 1.93 Å, Crystal structure of HLA-DR1/TPI(23-37) complexed with staphylococcal enterotoxin C3…
3BVG 2.0 Å, Manipulating the coupled folding and binding process drives affinity maturation in a…
3BVM 2.0 Å, Manipulating the coupled folding and binding process drives affinity maturation in a…
2AQ1 2.1 Å, Crystal structure of T-cell receptor V beta domain variant complexed with superantigen…
3BYY 2.2 Å, Manipulating the coupled folding and binding process drives affinity maturation in a…
1SJH 2.25 Å, HLA-DR1 complexed with a 13 residue HIV capsid peptide
1JWU 2.3 Å, Crystal Structure of the Complex of the MHC Class II Molecule HLA-DR1 (HA peptide…
2AQ3 2.3 Å, Crystal structure of T-cell receptor V beta domain variant complexed with superantigen…
2IPK 2.3 Å, Crystal Structure of the MHC Class II Molecule HLA-DR1 in Complex with the Fluorogenic…
3BVZ 2.3 Å, Manipulating the coupled folding and binding process drives affinity maturation in a…
3BZD 2.3 Å, Manipulating the coupled folding and binding process drives affinity maturation in a…

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