8VCX: Human TCR A2.13

Human TCR A2.13 in complex with DQ8-InsCpep. Determined by X-ray diffraction at 2.59 Å resolution. Released 7 Aug 2024.

Method: X-ray diffraction
Resolution: 2.59 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,553
Mol. weight: 96.83 kDa
Ligands: PO4
Released: 7 Aug 2024

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

Secondary structure: helices and β-sheets

8VCX contains 25 α-helices and 71 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: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	10
β-strand	19-26	8	10
β-strand	29-35	7	10
β-strand	40-43	4	10
α-helix	46-51	6
β-strand	53-54	2	11
α-helix	56-76	21
α-helix	81-85	5
β-strand	88-93	6	12
β-strand	103-112	10	12
β-strand	118-123	6	13
β-strand	126-128	3	13
β-strand	132-134	3	12
α-helix	137	1
β-strand	138-139	2	12
β-strand	145-153	9	12
β-strand	161-166	6	13
β-strand	174-178	5	13

Chain B: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	8-18	11	10
β-strand	23-32	10	10
β-strand	35-41	7	10
β-strand	47-49	3	10
α-helix	55-62	8
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-88	8
α-helix	90-92	3
β-strand	95	1	14
α-helix	96-97	2
β-strand	98-103	6	15
β-strand	113-122	10	15
β-strand	123	1	14
β-strand	128-133	6	16
β-strand	137-138	2	16
β-strand	142-144	3	15
α-helix	145-147	3
β-strand	148-149	2	15
β-strand	155-163	9	15
β-strand	170-176	7	16
β-strand	184-189	6	16

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	-1	1
β-strand	0-1	2	11
α-helix	6-9	4

Chain D: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	10-14	5	2
β-strand	19-24	6	1
β-strand	38-44	7	2
β-strand	51-56	6	2
β-strand	65-67	3	1
β-strand	77-80	4	1
β-strand	86-91	6	1
α-helix	96-98	3
β-strand	101-107	7	2
β-strand	120-125	6	2
β-strand	134-140	7	3
β-strand	147-152	6	3
β-strand	168-170	3	3
β-strand	176-178	3	4
β-strand	183-185	3	4
β-strand	187-192	6	3
α-helix	203-205	3
β-strand	213	1	3

Chain E: 8 helices, 24 β-strands

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-CELL-RECEPTOR, TCR A2.13 alpha	D	protein	203	Homo sapiens
T-CELL-RECEPTOR, A2.13-beta chain	E	protein	239	Homo sapiens
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)
Proinsulin C-peptide (InsC8-22)	C	protein	15	Homo sapiens	P01308 (AlphaFold model)

Sequence of entity 1 (D), FASTA

>8VCX_1 T-CELL-RECEPTOR, TCR A2.13 alpha (chains D)
MKTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMAS
LIITEDRKSSTLILPHATLRDTAVYYCIVSHNAGNMLTFGGGTRLMVKPHIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (E), FASTA

>8VCX_2 T-CELL-RECEPTOR, A2.13-beta chain (chains E)
GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPG
RFSGRQFSNSRSEMNVSTLELGDSALYLCASSLERETQYFGPGTRLLVLEDLKNVFPPEV
AVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALND
SRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Sequence of entity 3 (A), FASTA

>8VCX_3 MHC class II HLA-DQ-alpha chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPEI

Sequence of entity 4 (B), FASTA

>8VCX_4 MHC class II HLA-DQ-beta-1 (chains B)
RDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEY
WNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVT
DFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSL
QNPIIVEWRAQS

Sequence of entity 5 (C), FASTA

>8VCX_5 Proinsulin C-peptide (InsC8-22) (chains C)
GQVELGGGPGAESCQ

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

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
8VCY 2.6 Å, Human TCR A2.13 in complex with DQ8-InsC8-15NPY
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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