6DFW: TCR 8F10

TCR 8F10 in complex with IAg7-p8G9E. Determined by X-ray diffraction at 3.2 Å resolution. Released 17 Apr 2019.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Mus musculus
Chains: 8
Atoms: 12,219
Mol. weight: 192.97 kDa
Released: 17 Apr 2019

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

Secondary structure: helices and β-sheets

6DFW contains 31 α-helices and 140 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, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	1
β-strand	12-17	6	1
β-strand	21-22	2	1
β-strand	24-28	5	2
β-strand	31-37	7	2
β-strand	42-45	4	2
α-helix	49-53	5
β-strand	54-56	3	3
α-helix	59-78	20
α-helix	82-84	3
β-strand	90-95	6	4
β-strand	105-114	10	4
β-strand	120-125	6	5
β-strand	128-130	3	5
β-strand	134-136	3	4
β-strand	140-141	2	4
β-strand	147-155	9	4
β-strand	163-168	6	5
β-strand	176-180	5	5

Chain B: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	-26--24	3	3
α-helix	-23--18	6
β-strand	8-18	11	1
β-strand	26-33	8	1
β-strand	36-42	7	1
β-strand	48-50	3	1
α-helix	53-55	3
α-helix	56-65	10
α-helix	71-73	3
α-helix	74-78	5
α-helix	79-81	3
α-helix	82-86	5
α-helix	90-92	3
β-strand	103	1	6
β-strand	113-119	7	6
β-strand	128-133	6	7
β-strand	136-137	2	7
α-helix	138	1
β-strand	142	1	6
β-strand	157-163	7	6
β-strand	171-176	6	7
β-strand	184-188	5	7

Chain C: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	19
β-strand	12-17	6	19
β-strand	21-22	2	19
β-strand	24-28	5	20
β-strand	31-37	7	20
β-strand	42-45	4	20
α-helix	50-53	4
β-strand	54-55	2	21
α-helix	59-78	20
α-helix	82-87	6
β-strand	90-95	6	22
β-strand	100	1	23
β-strand	103	1	23
β-strand	105-114	10	22
β-strand	120-125	6	24
β-strand	128-130	3	24
β-strand	134-136	3	22
β-strand	140-141	2	22
β-strand	147-155	9	22
β-strand	163-168	6	24
β-strand	176-180	5	24

Chain D: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	-26--25	2	21
α-helix	-24	1
α-helix	-22--19	4
β-strand	8-18	11	19
β-strand	26-33	8	19
β-strand	36-42	7	19
β-strand	50	1	19
α-helix	53-55	3
α-helix	56-65	10
α-helix	68-73	6
α-helix	74-78	5
α-helix	79-81	3
α-helix	82-86	5
α-helix	90-92	3
β-strand	95	1	25
β-strand	103	1	26
β-strand	114-117	4	26
β-strand	120	1	27
β-strand	123	1	25
β-strand	128-133	6	28
β-strand	136-137	2	28
α-helix	138	1
β-strand	142-144	3	26
β-strand	156	1	27
β-strand	159-162	4	26
β-strand	171-176	6	28
β-strand	184-185	2	28

Chain E: 0 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	19-25	7	8
β-strand	31-32	2	9
β-strand	33-38	6	10
β-strand	44-50	7	10
β-strand	56-58	3	8
β-strand	62-67	6	8
β-strand	72-77	6	8
β-strand	87-90	4	10
β-strand	93-94	2	9
β-strand	124	1	11
β-strand	128-130	3	12
β-strand	141-142	2	11
β-strand	177-178	2	11

Chain F: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	13
β-strand	18-20	3	14
β-strand	30-37	8	15
β-strand	41-48	8	15
β-strand	55-56	2	15
β-strand	64-66	3	14
β-strand	74-77	4	14
α-helix	82-84	3
β-strand	87-88	2	13
β-strand	89-93	5	15
β-strand	101-102	2	15
β-strand	106-109	4	13
β-strand	118	1	16
β-strand	121-127	7	12
α-helix	129-134	6
β-strand	137-147	11	12
β-strand	148	1	16
β-strand	152-158	7	17
β-strand	162	1	17
β-strand	168-169	2	12
β-strand	174-175	2	12
β-strand	185-194	10	12
β-strand	204-211	8	17
β-strand	214	1	18
α-helix	225-227	3
β-strand	228	1	18
β-strand	230-237	8	17

Chain G: 0 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	29
β-strand	19-25	7	29
β-strand	33-38	6	30
β-strand	44-50	7	30
β-strand	56-59	4	29
β-strand	62-67	6	29
β-strand	72-77	6	29
β-strand	87-90	4	30
β-strand	110-111	2	30
β-strand	124-127	4	31
β-strand	129-130	2	32
β-strand	138-142	5	31
β-strand	149	1	33
β-strand	159-164	6	31
β-strand	177-181	5	31
β-strand	197	1	33
β-strand	203	1	31

Chain H: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	34
β-strand	18-20	3	35
β-strand	30-37	8	36
β-strand	41-50	10	36
β-strand	53-56	4	36
β-strand	64-66	3	35
β-strand	74-77	4	35
α-helix	82-84	3
β-strand	89-93	5	36
β-strand	101-102	2	36
β-strand	107-109	3	34
β-strand	118	1	37
β-strand	121-126	6	32
α-helix	129-135	7
β-strand	137-147	11	32
β-strand	148	1	37
β-strand	152-158	7	38
β-strand	161-162	2	38
β-strand	169	1	32
β-strand	174-175	2	32
β-strand	185-194	10	32
β-strand	204-211	8	38
α-helix	225-227	3
β-strand	230-237	8	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class II histocompatibility antigen, A-D alpha chain	A, C	protein	183	Mus musculus	P04228 (AlphaFold model)
H2-Ab1 protein	B, D	protein	221	Mus musculus	Q31135 (AlphaFold model)
8F10 alpha chain	E, G	protein	210	Mus musculus
8F10 beta chain	F, H	protein	241	Mus musculus

Sequence of entity 1 (A, C), FASTA

>6DFW_1 H-2 class II histocompatibility antigen, A-D alpha chain (chains A, C)
DIEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEPQG
GLQNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVIN
ITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHW
EPE

Sequence of entity 2 (B, D), FASTA

>6DFW_2 H2-Ab1 protein (chains B, D)
HLVERLYLVCGGEGAGGGSLVGGSGGGSERHFVHQFKGECYFTNGTQRIRLVTRYIYNRE
EYLRFDSDVGEYRAVTELGRHSAEYYNKQYLERTRAELDTACRHNYEETEVPTSLRRLEQ
PNVAISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQ
VLVMLEMTPHQGEVYTCHVEHPSLKSPITVEWRAQGGLVPR

Sequence of entity 3 (E, G), FASTA

>6DFW_3 8F10 alpha chain (chains E, G)
MEQVEQLPSILRVQEGSSASINCSYEDSASNYFPWYKQEPGENPKLIIDIRSNMERKQTQ
GLIVLLDKKAKRFSLHITDTQPGDSAMYFCAASRRGSGGSNYKLTFGKGTLLTVTPNIQN
PDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVA
WSNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (F, H), FASTA

>6DFW_4 8F10 beta chain (chains F, H)
MAVTQSPRNKVAVTGGKVTLSCDQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIP
DGYKASRPSQKEFSLILELATPSQTSVYFCASGGLGGDEQYFGPGTRLTVLEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

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 P04228 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BLQ 1.8 Å, Crystal Structure of IAg7 in complex with insulin mimotope p8E9E
7QHP 1.82 Å, Structure of I-Ag7 with a bound hybrid insulin peptide
6BLR 1.96 Å, Crystal Structure of IAg7 in complex with insulin mimotope p8E9E6SS
6BLX 2.32 Å, Crystal structure of IAg7 in complex with insulin mimotope p8G9E
2IAD 2.4 Å, Class II MHC I-ad in complex with an influenza hemagglutinin peptide 126-138
5DMK 2.45 Å, Crystal Structure of IAg7 in complex with RLGL-WE14
1ES0 2.6 Å, Crystal structure of the murine class II allele I-A(G7) complexed with the glutamic acid…
1IAO 2.6 Å, Class II MHC I-ad in complex with ovalbumin peptide 323-339
7Z50 2.65 Å, Structure of the highly diabetogenic 4.1-T cell receptor targeting a hybrid insulin…
3MBE 2.89 Å, TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27)
7RDV 2.9 Å, TFH TCR bound to MHC Class II IAd presenting aggrecan epitope
3CUP 3.09 Å, Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide…

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