6DFS: Mouse TCR I.29

mouse TCR I.29 in complex with IAg7-p8E9E6ss. Determined by X-ray diffraction at 3.1 Å resolution. Released 17 Apr 2019.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Mus musculus
Chains: 4
Atoms: 6,260
Mol. weight: 97.01 kDa
Ligands: NAG
Released: 17 Apr 2019

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

Secondary structure: helices and β-sheets

6DFS contains 14 α-helices and 76 β-strands across 4 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: 1 helix, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	32-38	7	2
β-strand	44-51	8	2
β-strand	56-59	4	1
β-strand	62-67	6	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	86-90	5	2
β-strand	91-92	2	3
β-strand	105-106	2	3
β-strand	111-115	5	2
β-strand	124-130	7	4
β-strand	137-142	6	4
β-strand	159-160	2	4
β-strand	166-168	3	5
β-strand	173-175	3	5
β-strand	177-181	5	4
β-strand	203	1	4

Chain B: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	6
β-strand	10-14	5	7
β-strand	18-25	8	6
β-strand	32	1	8
β-strand	34-38	5	7
β-strand	44-49	6	7
β-strand	56-61	6	6
β-strand	64-72	9	6
β-strand	75-81	7	6
β-strand	87-91	5	7
β-strand	92-93	2	9
β-strand	94	1	8
β-strand	102-103	2	9
β-strand	107-112	6	7
α-helix	115-117	3
β-strand	119	1	10
β-strand	122	1	5
β-strand	125	1	5
β-strand	126-127	2	4
α-helix	128-129	2
α-helix	130-136	7
β-strand	140-148	9	5
β-strand	149	1	10
β-strand	153-159	7	11
β-strand	163	1	11
β-strand	168-170	3	5
α-helix	174	1
β-strand	175-176	2	5
β-strand	186-193	8	5
α-helix	196-199	4
β-strand	205-212	8	11
β-strand	215	1	12
β-strand	229	1	12
β-strand	231	1	11
β-strand	234-238	5	11

Chain C: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	13
β-strand	13-17	5	13
β-strand	21-28	8	13
β-strand	32-37	6	13
β-strand	42-45	4	13
α-helix	49-51	3
β-strand	55-56	2	14
α-helix	59-76	18
β-strand	93-95	3	15
β-strand	105-114	10	15
β-strand	122-125	4	16
β-strand	128-130	3	16
β-strand	134-136	3	15
α-helix	137-138	2
β-strand	140-141	2	15
β-strand	147-155	9	15
β-strand	163-166	4	16
β-strand	177-179	3	16

Chain D: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	-25--24	2	14
α-helix	-21--18	4
β-strand	8-18	11	13
β-strand	25-33	9	13
β-strand	36-42	7	13
β-strand	47-50	4	13
α-helix	59-73	15
α-helix	74-79	6
α-helix	80-81	2
α-helix	82-86	5
β-strand	95	1	17
β-strand	117-122	6	18
β-strand	123	1	17
β-strand	148-149	2	18
β-strand	155-159	5	18
β-strand	174	1	19
β-strand	185	1	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
mouse TCR alpha chain	A	protein	210	Mus musculus
mouse TCR beta chain	B	protein	242	Mus musculus
H-2 class II histocompatibility antigen, A-D alpha chain	C	protein	183	Mus musculus	P04228 (AlphaFold model)
H2-Ab1 protein	D	protein	215	Mus musculus	Q31135 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6DFS_1 mouse TCR alpha chain (chains A)
MEKVEQHESTLSVREGDSAVINCTYTDTASSYFPWYKQEAGKGLHFVIDIRSNVDRKQSQ
RLIVLLDKKAKRFSLHITATQPEDSAIYFCAASPSNSGGSNYKLTFGKGTLLTVTPNIQN
PDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVA
WSNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (B), FASTA

>6DFS_2 mouse TCR beta chain (chains B)
MTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDAEVKS
LPGADYLATRVTDTELRLQVANMSQGRTLYCTCSAGLGYEQYFGPGTRLTVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Sequence of entity 3 (C), FASTA

>6DFS_3 H-2 class II histocompatibility antigen, A-D alpha chain (chains C)
DIEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEPQG
GLQCIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVIN
ITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHW
EPE

Sequence of entity 4 (D), FASTA

>6DFS_4 H2-Ab1 protein (chains D)
HLVERLYLVCGEEGAGGGSLVGGSGGGSERHFVHQFKGECYFTNGTQRIRLVTRYIYNRE
EYLRFDSDVGEYRAVTELGRHSAEYYNKQYLERTRAELDTACRHNYEETEVPTSLRRLEQ
PNVAISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQ
VLVMLEMTPHQGEVYTCHVEHPSLKSPITVEWRAQ

Ligands and cofactors

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

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…

Browse structure collections

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