8VCY: Human TCR A2.13

Human TCR A2.13 in complex with DQ8-InsC8-15NPY. Determined by X-ray diffraction at 2.6 Å resolution. Released 7 Aug 2024.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,519
Mol. weight: 96.16 kDa
Ligands: NAG, PO4
Released: 7 Aug 2024

Explore 8VCY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VCY contains 24 α-helices and 69 β-strands across 5 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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-51	6
α-helix	56-76	21
α-helix	81-87	7
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-122	5	3
β-strand	127	1	3
β-strand	132-134	3	2
β-strand	138-139	2	2
β-strand	145-153	9	2
β-strand	162-166	5	3
β-strand	174-177	4	3

Chain B: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	8-18	11	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-88	8
α-helix	90-92	3
β-strand	95	1	4
β-strand	98-103	6	5
β-strand	114-122	9	5
β-strand	123	1	4
β-strand	128-133	6	6
β-strand	136-138	3	6
β-strand	142-144	3	5
α-helix	145-147	3
β-strand	148-149	2	5
β-strand	155-162	8	5
β-strand	170-176	7	6
β-strand	184-189	6	6

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5

Chain D: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	7
β-strand	10-14	5	8
β-strand	19-24	6	7
β-strand	38-44	7	8
β-strand	51-56	6	8
β-strand	65-67	3	7
β-strand	77-80	4	7
β-strand	86-91	6	7
α-helix	96-98	3
β-strand	100-107	8	8
α-helix	112-114	3
β-strand	120-125	6	8
β-strand	134-137	4	9
α-helix	138	1
β-strand	139	1	10
α-helix	140-141	2
β-strand	149-152	4	9
α-helix	161-163	3
β-strand	168-170	3	9
β-strand	174-178	5	9
β-strand	183-192	10	9

Chain E: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-24	6	11
α-helix	25-26	2
β-strand	38-45	8	12
β-strand	49-57	9	12
β-strand	64-68	5	12
β-strand	76-80	5	11
β-strand	87-91	5	11
α-helix	96-98	3
β-strand	100-107	8	12
β-strand	114-115	2	12
β-strand	119-124	6	12
β-strand	131	1	13
α-helix	132-133	2
β-strand	134-138	5	14
β-strand	139	1	10
α-helix	140-141	2
α-helix	142-148	7
β-strand	150-160	11	14
β-strand	161	1	13
β-strand	165-171	7	15
β-strand	174-176	3	15
β-strand	180-182	3	14
α-helix	186	1
β-strand	187-188	2	14
β-strand	198-207	10	14
α-helix	208-211	4
β-strand	217-224	8	15
β-strand	227	1	16
α-helix	238-239	2
β-strand	241	1	16
β-strand	243-250	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class II HLA-DQ-alpha chain	A	protein	185	Homo sapiens	Q30069 (AlphaFold model)
MHC class II HLA-DQ-beta-1	B	protein	192	Homo sapiens	O19707 (AlphaFold model)
Hybrid insulin peptide (HIP; InsC8-15-NPY68-74)	C	protein	15	Homo sapiens
T-CELL-RECEPTOR, TCR A2.13 alpha	D	protein	203	Homo sapiens
T-CELL-RECEPTOR, TCR A2.13 beta	E	protein	239	Homo sapiens

Sequence of entity 1 (A), FASTA

>8VCY_1 MHC class II HLA-DQ-alpha chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPES

Sequence of entity 2 (B), FASTA

>8VCY_2 MHC class II HLA-DQ-beta-1 (chains B)
RDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEY
WNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVT
DFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSL
QNPIIVEWRAQS

Sequence of entity 3 (C), FASTA

>8VCY_3 Hybrid insulin peptide (HIP; InsC8-15-NPY68-74) (chains C)
GQVELGGGSSPETCI

Sequence of entity 4 (D), FASTA

>8VCY_4 T-CELL-RECEPTOR, TCR A2.13 alpha (chains D)
MKTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMAS
LIITEDRKSSTLILPHATLRDTAVYYCIVSHNAGNMLTFGGGTRLMVKPHIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>8VCY_5 T-CELL-RECEPTOR, TCR A2.13 beta (chains E)
GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPG
RFSGRQFSNSRSEMNVSTLELGDSALYLCASSLERETQYFGPGTRLLVLEDLKNVFPPEV
AVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALND
SRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
PO4	Phosphate ion	O4 P	4

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

Primary citation

A structural basis of T cell cross-reactivity to native and spliced self-antigens presented by HLA-DQ8. Tran, M.T., Lim, J.J., Loh, T.J. et al. J Biol Chem (2024) 300:107612-107612. DOI 10.1016/j.jbc.2024.107612 · PubMed

Other PDB entries of the same protein (UniProt Q30069 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DFX 2.03 Å, human diabetogenic TCR T1D3 in complex with DQ8-p8E9E peptide
6XC9 2.4 Å, Immune receptor complex
8VD0 2.4 Å, Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP2
5KS9 2.55 Å, Bel502-DQ8-glia-alpha1 complex
8VCX 2.59 Å, Human TCR A2.13 in complex with DQ8-InsCpep
8VDD 2.6 Å, Crystal structure of Proinsulin C-peptide bound to HLA-DQ8
4Z7V 2.65 Å, L3-12 complex
4Z7U 2.7 Å, S13 complex
4Z7W 2.89 Å, T316 complex
6XCO 2.9 Å, Immune receptor complex
8VD2 2.9 Å, Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP1
6XCP 3.3 Å, Immune receptor complex

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