6DFX: Human diabetogenic TCR T1D3

human diabetogenic TCR T1D3 in complex with DQ8-p8E9E peptide. Determined by X-ray diffraction at 2.03 Å resolution. Released 17 Apr 2019.

Method: X-ray diffraction
Resolution: 2.03 Å
Organism: Homo sapiens
Chains: 8
Atoms: 13,693
Mol. weight: 193.2 kDa
Ligands: NAG
Released: 17 Apr 2019

Explore 6DFX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DFX contains 45 α-helices and 136 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: 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	80-83	4
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-123	6	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	161-166	6	3
β-strand	174-177	4	3

Chain B: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	-22--17	6
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	81-87	7
α-helix	90-92	3
β-strand	95	1	4
α-helix	96-97	2
β-strand	98-102	5	5
β-strand	115-122	8	5
β-strand	123	1	4
β-strand	128-133	6	6
β-strand	136-137	2	6
α-helix	138	1
β-strand	142-144	3	5
β-strand	148-149	2	5
β-strand	155-161	7	5
β-strand	171-176	6	6
β-strand	184-188	5	6

Chain D: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	7
β-strand	19-26	8	7
β-strand	29-35	7	7
β-strand	40-43	4	7
α-helix	46-51	6
α-helix	56-76	21
α-helix	81-85	5
β-strand	88-93	6	8
β-strand	103-112	10	8
β-strand	118-123	6	9
β-strand	126-128	3	9
β-strand	132-134	3	8
β-strand	138-139	2	8
β-strand	145-153	9	8
β-strand	161-166	6	9
β-strand	174-177	4	9

Chain E: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	-22--17	6
β-strand	8-18	11	7
β-strand	23-32	10	7
β-strand	35-41	7	7
β-strand	47-49	3	7
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	10
α-helix	96-97	2
β-strand	98-102	5	11
β-strand	114-122	9	11
β-strand	123	1	10
β-strand	128-133	6	12
β-strand	136-137	2	12
α-helix	138	1
β-strand	142-144	3	11
α-helix	145-147	3
β-strand	148-149	2	11
β-strand	155-162	8	11
β-strand	171-176	6	12
β-strand	184-188	5	12

Chain G: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	13
β-strand	18-23	6	14
β-strand	30-36	7	13
β-strand	42-49	8	13
β-strand	54-57	4	14
β-strand	60-65	6	14
β-strand	70-75	6	14
α-helix	80-82	3
β-strand	84-90	7	13
β-strand	101-102	2	13
β-strand	106-111	6	13
β-strand	120-123	4	15
β-strand	133-138	6	15
β-strand	155-156	2	15
α-helix	157-159	3
β-strand	160-164	5	15
α-helix	165-167	3
β-strand	169-178	10	15
β-strand	199	1	15

Chain H: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	16
β-strand	10-14	5	17
β-strand	19-24	6	16
α-helix	25-26	2
β-strand	31-38	8	17
β-strand	42-50	9	17
β-strand	53-57	5	17
β-strand	64-68	5	16
β-strand	74-78	5	16
α-helix	83-85	3
β-strand	87-94	8	17
β-strand	99-107	3	17
β-strand	111-116	6	17
α-helix	119-121	3
β-strand	123	1	18
α-helix	124-125	2
β-strand	126-130	5	19
α-helix	131-133	3
α-helix	134-139	6
β-strand	142-152	11	19
β-strand	153	1	18
β-strand	157-163	7	20
β-strand	166-168	3	20
β-strand	172-174	3	19
α-helix	178	1
β-strand	179-180	2	19
β-strand	190-199	10	19
α-helix	200-204	5
β-strand	209-216	8	20
β-strand	219	1	21
β-strand	233	1	21
β-strand	235-242	8	20

Chain I: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	22
β-strand	18-23	6	23
β-strand	30-36	7	22
α-helix	37	1
β-strand	42-49	8	22
β-strand	54-57	4	23
β-strand	60-65	6	23
β-strand	70-75	6	23
α-helix	80-82	3
β-strand	84-90	7	22
β-strand	101-102	2	22
β-strand	106-111	6	22
β-strand	120-123	4	24
β-strand	133-138	6	24
β-strand	155-156	2	24
β-strand	161-162	2	25
β-strand	173-178	6	24
α-helix	185-188	4
β-strand	199	1	24

Chain J: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	26
β-strand	10-14	5	27
β-strand	19-24	6	26
α-helix	25-26	2
β-strand	31-38	8	27
β-strand	42-50	9	27
β-strand	53-57	5	27
β-strand	64-68	5	26
β-strand	74-78	5	26
α-helix	83-85	3
β-strand	87-94	8	27
β-strand	99-101	3	27
β-strand	105-110	6	27
α-helix	113-115	3
β-strand	117	1	28
α-helix	118-119	2
β-strand	120-124	5	25
α-helix	125-127	3
α-helix	128-134	7
β-strand	136-146	11	25
β-strand	147	1	28
β-strand	151-157	7	29
β-strand	160-162	3	29
β-strand	166-168	3	25
β-strand	173-174	2	25
β-strand	184-193	10	25
α-helix	194-198	5
β-strand	203-210	8	29
β-strand	213	1	30
α-helix	224-225	2
β-strand	227	1	30
β-strand	229-236	8	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class II HLA-DQ-alpha chain	A, D	protein	188	Homo sapiens	Q30069 (AlphaFold model)
MHC class II antigen	B, E	protein	221	Homo sapiens	U3PYM0 (AlphaFold model)
T1D3 alpha chain	G, I	protein	207	Homo sapiens
T1D3 beta chain	H, J	protein	238	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>6DFX_1 MHC class II HLA-DQ-alpha chain (chains A, D)
IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA
LTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI
TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWE
PEGGLVPR

Sequence of entity 2 (B, E), FASTA

>6DFX_2 MHC class II antigen (chains B, E)
VEELYLVAGEEGCGGGGSLVGGSGGGSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREE
YARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVE
PTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQ
ILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRAQGGLVPR

Sequence of entity 3 (G, I), FASTA

>6DFX_3 T1D3 alpha chain (chains G, I)
MQQGEEDPQALSIQEGENATMNCSYKTSINNLQWYRQNSGRGLVHLILIRSNEREKHSGR
LRVTLDTSKKSSSLLITASRAADTASYFCATDAGYNQGGKLIFGQGTELSVKPNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (H, J), FASTA

>6DFX_4 T1D3 beta chain (chains H, J)
GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPG
RFSGRQFSNSRSEMNVSTLELGDSALYLCASSAGNTIYFGEGSWLTVVEDLKNVFPPEVA
VFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDS
RYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Ligands and cofactors

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

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

Primary citation

How C-terminal additions to insulin B-chain fragments create superagonists for T cells in mouse and human type 1 diabetes. Wang, Y., Sosinowski, T., Novikov, A. et al. Sci Immunol (2019) 4. DOI 10.1126/sciimmunol.aav7517 · PubMed

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

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
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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