1L0Y: T cell receptor beta chain

T cell receptor beta chain complexed with superantigen SpeA soaked with zinc. Determined by X-ray diffraction at 2.5 Å resolution. Released 3 Apr 2002.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Mus musculus, Streptococcus pyogenes
Chains: 4
Atoms: 7,421
Mol. weight: 104.86 kDa
Ligands: ZN
Released: 3 Apr 2002

Explore 1L0Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1L0Y contains 32 α-helices and 86 β-strands across 4 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: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	31-37	7	2
β-strand	43-49	7	2
β-strand	56-57	2	2
β-strand	66-68	3	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	88-95	8	2
α-helix	101-105	3
β-strand	106-108	3	2
β-strand	112-250	6	2
α-helix	119-121	3
β-strand	123	1	3
β-strand	126-130	5	4
α-helix	131-133	3
α-helix	134-138	5
β-strand	142-152	11	4
β-strand	153	1	3
β-strand	157-163	7	5
β-strand	166-168	3	5
β-strand	172-174	3	4
α-helix	178	1
β-strand	179-182	4	4
β-strand	189-199	11	4
α-helix	202-204	3
β-strand	209-216	8	5
β-strand	219	1	6
β-strand	233	1	6
β-strand	235-242	8	5

Chain B: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	10-11	2
α-helix	12-14	3
α-helix	19-26	8
α-helix	28-29	2
β-strand	30-35	6	7
β-strand	39	1	8
β-strand	45-48	4	8
β-strand	52	1	9
β-strand	55	1	9
β-strand	57-61	5	8
α-helix	65-71	7
β-strand	76-80	5	7
β-strand	83	1	8
β-strand	96-100	5	8
β-strand	103-105	3	7
β-strand	110-123	14	10
β-strand	126-137	12	10
β-strand	139-141	3	11
α-helix	142-157	16
β-strand	161	1	12
β-strand	163	1	12
β-strand	169-176	8	10
β-strand	182-185	4	10
α-helix	194-197	4
α-helix	198-201	4
β-strand	206-208	3	11
β-strand	212-219	8	10

Chain C: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	2
β-strand	19-25	7	13
β-strand	31-37	7	2
β-strand	43-49	7	2
β-strand	56-57	2	2
β-strand	66-68	3	13
β-strand	74-79	6	13
α-helix	84-86	3
β-strand	88-95	8	2
α-helix	101-105	3
β-strand	106-108	3	2
β-strand	112-250	6	2
α-helix	119-121	3
β-strand	123	1	14
β-strand	126-130	5	15
α-helix	131-133	3
α-helix	134-138	5
β-strand	142-152	11	15
β-strand	153	1	14
β-strand	157-163	7	16
β-strand	166-168	3	16
β-strand	172-174	3	15
α-helix	178	1
β-strand	179-182	4	15
β-strand	189-199	11	15
β-strand	209-216	8	16
β-strand	219	1	17
β-strand	233	1	17
β-strand	235-242	8	16

Chain D: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	6-8	3
α-helix	10-11	2
α-helix	12-14	3
α-helix	19-26	8
α-helix	28-29	2
β-strand	30-35	6	18
β-strand	39	1	19
β-strand	45-48	4	19
β-strand	52	1	20
β-strand	55	1	20
β-strand	57-61	5	19
α-helix	65-71	7
β-strand	76-80	5	18
β-strand	83	1	19
β-strand	96-100	5	19
β-strand	103-105	3	18
β-strand	110-123	14	21
β-strand	126-137	12	21
β-strand	139-141	3	22
α-helix	142-157	16
β-strand	161	1	23
β-strand	163	1	23
β-strand	167-176	10	21
β-strand	182-185	4	21
α-helix	194-197	4
α-helix	198-201	4
β-strand	206-208	3	22
β-strand	212-220	9	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
14.3.d T cell receptor beta chain	A, C	protein	236	Mus musculus	P01851 (AlphaFold model)
Exotoxin type A	B, D	protein	221	Streptococcus pyogenes	P0DJY7 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1L0Y_1 14.3.d T cell receptor beta chain (chains A, C)
AVTQSPRNKVAVTGGKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPD
GYKASRPSQEQFSLILELATPSQTSVYFCASGGGRGSYAEQFFGPGTRLTVLEDLRQVTP
PKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNY
SYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGR

Sequence of entity 2 (B, D), FASTA

>1L0Y_2 Exotoxin type A (chains B, D)
QQDPDPSQLHRSSLVKNLQNIYFLYEGDPVTHENVKSVDQLLSHDLIYNVSGPNYDKLKT
ELKNQEMATLFKDKNVDIYGVEYYHLCYLSENAERSACIYGGVTNHEGNHLEIPKKIVVK
VSIDGIQSLSFDIETNKKMVTAQELDYKVRKYLTDNKQLYTNGPSKYETGYIKFIPKNKE
SFWFDFFPEPEFTQSKYLMIYKDNETLDSNTSQIEVYLTTK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structures of two streptococcal superantigens bound to TCR beta chains reveal diversity in the architecture of T cell signaling complexes. Sundberg, E.J., Li, H., Llera, A.S. et al. Structure (2002) 10:687-699. DOI 10.1016/S0969-2126(02)00759-1 · PubMed

Other PDB entries of the same protein (UniProt P01851 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1BEC 1.7 Å, Beta chain of a T cell antigen receptor
5M02 1.75 Å, Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
2Q86 1.85 Å, Structure of the mouse invariant NKT cell receptor Valpha14
5M01 1.95 Å, Crystal structure of murine P14 TCR/ H-2Db complex with PA, modified gp33 peptide from…
1MWA 2.4 Å, 2C/H-2KBM3/DEV8 allogeneic complex
1L0X 2.8 Å, TCR beta chain complexed with streptococcal superantigen SpeA

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