7Z50: PDB entry 7Z50

Structure of the highly diabetogenic 4.1-T cell receptor targeting a hybrid insulin peptide bound to I-Ag7. Determined by X-ray diffraction at 2.65 Å resolution. Released 20 Jul 2022.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: Mus musculus
Chains: 10
Atoms: 12,716
Mol. weight: 204.27 kDa
Ligands: NAG
Released: 20 Jul 2022

Explore 7Z50 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z50 contains 48 α-helices and 141 β-strands across 10 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6-17	12	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	42-45	4	1
α-helix	48-53	6
β-strand	55	1	2
α-helix	59-78	20
α-helix	82-87	6
β-strand	90-95	6	3
β-strand	105-114	10	3
β-strand	120-125	6	4
β-strand	128-130	3	4
β-strand	134-136	3	3
β-strand	140-141	2	3
β-strand	147-155	9	3
β-strand	163-168	6	4
β-strand	176-180	5	4

Chain B: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	52-54	3
α-helix	55-64	10
α-helix	66-72	7
α-helix	73-78	6
α-helix	79-80	2
α-helix	81-85	5
α-helix	86-88	3
β-strand	94	1	5
β-strand	97-102	6	6
β-strand	113-121	9	6
β-strand	122	1	5
β-strand	127-132	6	7
β-strand	135-137	3	7
β-strand	141-143	3	6
α-helix	144-146	3
β-strand	147-148	2	6
β-strand	154-161	8	6
β-strand	170-175	6	7
β-strand	183-187	5	7

Chain C: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	8
β-strand	13-17	5	8
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	42-45	4	8
α-helix	48-53	6
β-strand	55	1	9
α-helix	59-78	20
α-helix	83-87	5
β-strand	90-95	6	10
β-strand	105-114	10	10
β-strand	120-125	6	11
β-strand	128-129	2	11
β-strand	134-136	3	10
β-strand	140-141	2	10
β-strand	147-155	9	10
β-strand	163-168	6	11
β-strand	176-180	5	11

Chain D: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	8
β-strand	23-32	10	8
β-strand	35-41	7	8
β-strand	46-49	4	8
α-helix	52-54	3
α-helix	55-64	10
α-helix	66-72	7
α-helix	73-78	6
α-helix	79-80	2
α-helix	81-85	5
α-helix	86-88	3
β-strand	94	1	12
β-strand	97-102	6	13
β-strand	113-121	9	13
β-strand	122	1	12
β-strand	127-132	6	14
β-strand	135-137	3	14
β-strand	141-143	3	13
α-helix	144-146	3
β-strand	147-148	2	13
β-strand	154-161	8	13
β-strand	170-175	6	14
β-strand	183-186	4	14

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	15
β-strand	9-13	5	16
β-strand	18-23	6	15
α-helix	24-25	2
β-strand	30-37	8	16
β-strand	41-49	9	16
β-strand	52-55	4	16
β-strand	64-67	4	15
β-strand	74-78	5	15
α-helix	83-85	3
β-strand	87-94	8	16
β-strand	102-103	2	16
β-strand	107-112	6	16
α-helix	115-117	3
β-strand	119	1	17
α-helix	120-121	2
β-strand	122-126	5	18
α-helix	127-129	3
α-helix	130-136	7
β-strand	138-148	11	18
β-strand	149	1	17
β-strand	153-159	7	19
β-strand	162-164	3	19
β-strand	168-170	3	18
β-strand	175-176	2	18
β-strand	186-195	10	18
α-helix	196-200	5
β-strand	205-212	8	19
β-strand	215	1	20
α-helix	226-227	2
β-strand	229	1	20
β-strand	231-238	8	19

Chain F: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	21
β-strand	9-13	5	22
β-strand	18-23	6	21
α-helix	24-25	2
β-strand	30-37	8	22
β-strand	41-49	9	22
β-strand	52-55	4	22
α-helix	60	1
β-strand	64-67	4	21
β-strand	74-78	5	21
α-helix	83-85	3
β-strand	87-94	8	22
β-strand	102-103	2	22
β-strand	107-112	6	22
α-helix	115-117	3
β-strand	119	1	23
α-helix	120-121	2
β-strand	122-126	5	24
α-helix	127-129	3
α-helix	130-136	7
β-strand	138-148	11	24
β-strand	149	1	23
β-strand	153-159	7	25
β-strand	162-164	3	25
β-strand	168-170	3	24
α-helix	174	1
β-strand	175-176	2	24
β-strand	186-195	10	24
α-helix	196-200	5
β-strand	205-212	8	25
β-strand	215	1	26
α-helix	226-227	2
β-strand	229	1	26
β-strand	231-238	8	25

Chain G: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	27
β-strand	11-15	5	28
β-strand	20-26	7	27
β-strand	33-39	7	28
β-strand	46-52	7	28
β-strand	57-59	3	27
β-strand	63-68	6	27
β-strand	73-78	6	27
α-helix	83-85	3
β-strand	87-94	8	28
β-strand	100-102	3	28
β-strand	106-111	6	28
β-strand	120-124	5	29
α-helix	125-126	2
β-strand	133-138	6	29
β-strand	154-156	3	29
α-helix	157-159	3
β-strand	160-164	5	29
β-strand	169-178	10	29

Chain H: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	30
β-strand	11-15	5	31
β-strand	20-26	7	30
β-strand	33-39	7	31
β-strand	46-52	7	31
β-strand	57-59	3	30
β-strand	63-68	6	30
β-strand	73-78	6	30
α-helix	83-85	3
β-strand	87-94	8	31
β-strand	100-102	3	31
β-strand	106-111	6	31
β-strand	120-124	5	32
α-helix	125-127	3
β-strand	133-140	8	32
β-strand	154-156	3	32
α-helix	157-159	3
β-strand	160-163	4	32
β-strand	170-178	9	32

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class II histocompatibility antigen, A-D alpha chain	A, C	protein	202	Mus musculus	P04228 (AlphaFold model)
H2-Ab1 protein	B, D	protein	230	Mus musculus	Q31135 (AlphaFold model)
4.1 TCR beta chain	E, F	protein	242	Mus musculus
4.1 TCR alpha chain	G, H	protein	207	Mus musculus
Hybrid insulin peptide	T, W	protein	15	Mus musculus

Sequence of entity 1 (A, C), FASTA

>7Z50_1 H-2 class II histocompatibility antigen, A-D alpha chain (chains A, C)
EDDIEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEP
QGGLQNIAAEKHNLGCLTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPV
INITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLK
HWEPEIPAPMSELTESLEVLFQ

Sequence of entity 2 (B, D), FASTA

>7Z50_2 H2-Ab1 protein (chains B, D)
LQTLALEVEDDPCGGGGGSGGGSGGSGDSERHFVHQFKGECYFTNGTQRIRLVTRYIYNR
EEYLRFDSDVGEYRAVTELGRHSAEYYNKQYLERTRAELDTACRHNYEETEVPTSLRRLE
QPNVAISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTF
QVLVMLEMTPHQGEVYTCHVEHPSLKSPITVEWRAQSESARSKSLEVLFQ

Sequence of entity 3 (E, F), FASTA

>7Z50_3 4.1 TCR beta chain (chains E, F)
MGVIQTPRHKVTGKGQEATLWCEPISGHSAVFWYRQTIVQGLEFLTYFRNQAPIDDSGMP
KERFSAQMPNQSHSTLKIQSTQPQDSAVYLCASSRQGQNTLYFGAGTRLSVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Sequence of entity 4 (G, H), FASTA

>7Z50_4 4.1 TCR alpha chain (chains G, H)
MGEQVEQLPSILRVQEGSSASINCSYEDSASNYFPWYKQEPGENPKLIIDIRSNMERKQT
QGLIVLLDKKAKRFSLHITDTQPGDSAMYFCAASVRNYKYVFGAGTRLKVIADIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESSA

Sequence of entity 5 (T, W), FASTA

>7Z50_5 Hybrid insulin peptide (chains T, W)
LQTLALEVEDDPCGG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

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

Primary citation

Structural plasticity in I-A g7 links autoreactivity to hybrid insulin peptides in type I diabetes. Erausquin, E., Serra, P., Parras, D. et al. Front Immunol (2022) 13:924311-924311. DOI 10.3389/fimmu.2022.924311 · 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
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…
1F3J 3.1 Å, Histocompatibility antigen I-AG7

Browse structure collections

About this viewer

MolViewer shows 7Z50 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.