8VD2: Human TCR ET650-4

Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP1. Determined by X-ray diffraction at 2.9 Å resolution. Released 7 Aug 2024.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,323
Mol. weight: 95.53 kDa
Ligands: NAG
Released: 7 Aug 2024

Explore 8VD2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VD2 contains 18 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: 2 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
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	117-123	7	3
β-strand	126-128	3	3
β-strand	132-134	3	2
β-strand	138-139	2	2
β-strand	145-153	9	2
β-strand	161-167	7	3
β-strand	174-177	4	3

Chain B: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
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
α-helix	96-97	2
β-strand	98-103	6	5
β-strand	114-122	9	5
β-strand	123	1	4
β-strand	128-132	5	6
β-strand	137	1	6
β-strand	142-144	3	5
β-strand	148-149	2	5
β-strand	155-162	8	5
β-strand	172-177	6	6
β-strand	180-187	8	6

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	-1	1	7

Chain D: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	10-14	5	9
β-strand	19-24	6	8
β-strand	38-44	7	9
α-helix	49-50	2
β-strand	51-56	6	9
β-strand	66-67	2	8
β-strand	77-80	4	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	100-107	8	9
β-strand	110	1	7
β-strand	123-128	6	9
β-strand	137-143	7	10
β-strand	150-155	6	10
α-helix	164-166	3
β-strand	171-173	3	10
β-strand	177-181	5	10
β-strand	186-195	10	10

Chain E: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-24	6	11
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	115-116	2	12
β-strand	120-125	6	12
α-helix	128-130	3
β-strand	132	1	13
α-helix	133-134	2
β-strand	135-140	6	10
α-helix	141-142	2
α-helix	143-149	7
β-strand	151-161	11	10
β-strand	162	1	13
β-strand	166-172	7	14
β-strand	175-177	3	14
β-strand	181-183	3	10
β-strand	188-189	2	10
β-strand	199-208	10	10
α-helix	209-212	4
β-strand	218-225	8	14
β-strand	239	1	15
α-helix	250-251	2
β-strand	253	1	15
β-strand	255-262	8	14

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-IAPP23-29 )	C	protein	15	Homo sapiens
T-CELL-RECEPTOR, TCR ET650-4 alpha	D	protein	206	Homo sapiens
T-CELL-RECEPTOR, TCR ET650-4 beta	E	protein	240	Homo sapiens

Sequence of entity 1 (A), FASTA

>8VD2_1 MHC class II HLA-DQ-alpha chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPEI

Sequence of entity 2 (B), FASTA

>8VD2_2 MHC class II HLA-DQ-beta-1 (chains B)
RDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEY
WNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVT
DFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSL
QNPIIVEWRAQS

Sequence of entity 3 (C), FASTA

>8VD2_3 Hybrid insulin peptide (HIP; InsC8-15-IAPP23-29 ) (chains C)
GQVELGGGTPIESCQ

Sequence of entity 4 (D), FASTA

>8VD2_4 T-CELL-RECEPTOR, TCR ET650-4 alpha (chains D)
MKTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMAS
LIITEDRKSSTLILPHATLRDTAVYYCIVRVAIEGSQGNLIFGKGTKLSVKPNIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>8VD2_5 T-CELL-RECEPTOR, TCR ET650-4 beta (chains E)
GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPG
RFSGRQFSNSRSEMNVSTLELGDSALYLCASSLRRGDTIYFGEGSWLTVVEDLNKVFPPE
VAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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
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
6XCP 3.3 Å, Immune receptor complex

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