8VD0: Human TCR ET650-4

Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP2. Determined by X-ray diffraction at 2.4 Å resolution. Released 7 Aug 2024.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 8
Atoms: 13,282
Mol. weight: 194.13 kDa
Ligands: PO4, NAG
Released: 7 Aug 2024

Explore 8VD0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VD0 contains 55 α-helices and 146 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: 6 helices, 14 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
β-strand	54	1	2
α-helix	56-76	21
α-helix	81-85	5
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	118-123	6	4
β-strand	126-128	3	4
β-strand	132-134	3	3
α-helix	137	1
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
α-helix	173	1
β-strand	174-177	4	4
α-helix	178-179	2

Chain C: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	-1	1	5
β-strand	1	1	2
α-helix	4-9	6
β-strand	26-36	11	1
β-strand	41-50	10	1
β-strand	53-59	7	1
β-strand	65-67	3	1
α-helix	73-81	9
α-helix	83-92	10
α-helix	93-98	6
α-helix	99-106	8
α-helix	108-110	3
β-strand	113	1	6
α-helix	114-115	2
β-strand	116-120	5	7
β-strand	132-140	9	7
β-strand	141	1	6
β-strand	146-151	6	8
β-strand	154-155	2	8
β-strand	160-162	3	7
α-helix	163-165	3
β-strand	166-167	2	7
β-strand	173-180	8	7
β-strand	189-194	6	8
β-strand	202-205	4	8

Chain D: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	18
β-strand	10-14	5	19
α-helix	18	1
β-strand	19-24	6	18
β-strand	38-44	7	19
α-helix	49-50	2
β-strand	51-56	6	19
β-strand	66-67	2	18
β-strand	77-80	4	18
β-strand	86-91	6	18
α-helix	96-98	3
β-strand	100-107	8	19
β-strand	110	1	5
β-strand	123-128	6	19
β-strand	137-143	7	20
β-strand	150-155	6	20
α-helix	164-166	3
β-strand	171-173	3	20
α-helix	174-176	3
β-strand	177-181	5	20
α-helix	182-184	3
β-strand	186-195	10	20
β-strand	216	1	20

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	21
β-strand	10-14	5	22
β-strand	19-24	6	21
α-helix	25-26	2
β-strand	38-45	8	22
β-strand	49-57	9	22
β-strand	64-68	5	22
β-strand	76-80	5	21
β-strand	87-91	5	21
α-helix	96-98	3
β-strand	100-107	8	22
α-helix	113-114	2
β-strand	115-116	2	22
β-strand	120-125	6	22
α-helix	128-130	3
β-strand	132	1	23
β-strand	135-140	6	20
α-helix	141-142	2
α-helix	143-149	7
β-strand	151-161	11	20
β-strand	162	1	23
β-strand	166-172	7	24
β-strand	175-177	3	24
β-strand	181-183	3	20
β-strand	188-189	2	20
β-strand	199-208	10	20
α-helix	209-213	5
β-strand	218-225	8	24
β-strand	239	1	25
α-helix	250-251	2
β-strand	253	1	25
β-strand	255-262	8	24

Chain F: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	9
β-strand	19-26	8	9
β-strand	29-35	7	9
β-strand	40-43	4	9
α-helix	46-51	6
β-strand	54	1	10
α-helix	56-76	21
α-helix	81-87	7
β-strand	88-93	6	11
β-strand	98	1	12
β-strand	101	1	12
β-strand	103-112	10	11
β-strand	118-123	6	13
β-strand	126-128	3	13
β-strand	132-134	3	11
α-helix	137	1
β-strand	138-139	2	11
β-strand	145-153	9	11
β-strand	161-166	6	13
β-strand	174-177	4	13

Chain H: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	-1	1	14
β-strand	1	1	10
α-helix	4-9	6
β-strand	26-36	11	9
β-strand	41-50	10	9
β-strand	53-59	7	9
β-strand	65-67	3	9
α-helix	73-81	9
α-helix	83-92	10
α-helix	93-98	6
α-helix	99-106	8
α-helix	108-110	3
β-strand	113	1	15
α-helix	114-115	2
β-strand	116-120	5	16
β-strand	132-140	9	16
β-strand	141	1	15
β-strand	146-151	6	17
β-strand	154-155	2	17
β-strand	160-162	3	16
α-helix	163-165	3
β-strand	166-167	2	16
β-strand	173-180	8	16
β-strand	189-194	6	17
β-strand	202-206	5	17

Chain I: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	26
β-strand	10-14	5	27
α-helix	18	1
β-strand	19-24	6	26
β-strand	38-44	7	27
α-helix	49-50	2
β-strand	51-56	6	27
β-strand	65-67	3	26
β-strand	77-80	4	26
β-strand	86-91	6	26
α-helix	96-98	3
β-strand	100-107	8	27
β-strand	110	1	14
β-strand	123-128	6	27
β-strand	137-143	7	28
β-strand	150-155	6	28
α-helix	164-166	3
β-strand	171-173	3	28
β-strand	177-181	5	28
β-strand	186-195	10	28
α-helix	202-204	3
α-helix	211-212	2
β-strand	216	1	28

Chain J: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	29
β-strand	10-14	5	30
β-strand	19-24	6	29
α-helix	25	1
β-strand	38-45	8	30
β-strand	49-57	9	30
β-strand	64-68	5	30
β-strand	76-80	5	29
β-strand	87-91	5	29
α-helix	96-98	3
β-strand	100-107	8	30
α-helix	113-114	2
β-strand	115-116	2	30
β-strand	120-125	6	30
α-helix	128-130	3
β-strand	132	1	31
α-helix	133-134	2
β-strand	135-140	6	28
α-helix	141-142	2
α-helix	143-149	7
β-strand	151-161	11	28
β-strand	162	1	31
β-strand	166-172	7	32
β-strand	175-177	3	32
β-strand	181-183	3	28
β-strand	188-189	2	28
β-strand	199-208	10	28
α-helix	209-212	4
β-strand	218-225	8	32
β-strand	239	1	33
α-helix	250-251	2
β-strand	253	1	33
β-strand	255-262	8	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class II HLA-DQ-alpha chain	A, F	protein	185	Homo sapiens	Q30069 (AlphaFold model)
Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80),MHC class II HLA-DQ-beta-1 chimera	C, H	protein	213	Homo sapiens	O19707 (AlphaFold model)
T-CELL-RECEPTOR, TCR ET650-4 alpha	D, I	protein	206	Homo sapiens
T-CELL-RECEPTOR, TCR ET650-4 beta	E, J	protein	240	Homo sapiens

Sequence of entity 1 (A, F), FASTA

>8VD0_1 MHC class II HLA-DQ-alpha chain (chains A, F)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPEI

Sequence of entity 2 (C, H), FASTA

>8VD0_2 Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80),MHC class II HLA-DQ-beta-1 chimera (chains C, H)
GQVELGGGNAVEVCKGGSGGSRDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYAR
FDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTV
TISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILV
MLEMTPQRGDVYTCHVEHPSLQNPIIVEWRAQS

Sequence of entity 3 (D, I), FASTA

>8VD0_3 T-CELL-RECEPTOR, TCR ET650-4 alpha (chains D, I)
MKTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMAS
LIITEDRKSSTLILPHATLRDTAVYYCIVRVAIEGSQGNLIFGKGTKLSVKPNIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E, J), FASTA

>8VD0_4 T-CELL-RECEPTOR, TCR ET650-4 beta (chains E, J)
GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPG
RFSGRQFSNSRSEMNVSTLELGDSALYLCASSLRRGDTIYFGEGSWLTVVEDLNKVFPPE
VAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	6
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

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
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
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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