5DMK: IAg7

Crystal Structure of IAg7 in complex with RLGL-WE14. Determined by X-ray diffraction at 2.45 Å resolution. Released 28 Oct 2015.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Mus musculus
Chains: 8
Atoms: 12,200
Mol. weight: 178.72 kDa
Ligands: FLC
Released: 28 Oct 2015

Explore 5DMK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DMK contains 45 α-helices and 107 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: 2 helices, 12 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	59-78	20
α-helix	83-86	4
β-strand	90-95	6	2
β-strand	105-114	10	2
β-strand	120-125	6	3
β-strand	128-130	3	3
β-strand	134-136	3	2
β-strand	140-141	2	2
β-strand	147-155	9	2
β-strand	163-168	6	3

Chain B: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-19	12	1
β-strand	24-33	10	1
β-strand	36-42	7	1
β-strand	47-50	4	1
α-helix	53-55	3
α-helix	56-75	18
α-helix	76-81	6
α-helix	82-83	2
α-helix	84-88	5
α-helix	92-94	3
β-strand	98	1	4
α-helix	99-100	2
β-strand	101-106	6	5
β-strand	116-125	10	5
β-strand	126	1	4
β-strand	131-136	6	6
β-strand	139-140	2	6
β-strand	145-148	4	5
α-helix	149-150	2
β-strand	151-152	2	5
β-strand	158-166	9	5
β-strand	174-179	6	6
β-strand	187-191	5	6

Chain C: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-17	12	7
β-strand	21-28	8	7
β-strand	31-37	7	7
β-strand	42-45	4	7
α-helix	59-78	20
α-helix	86-89	4
β-strand	90-95	6	8
β-strand	105-114	10	8
β-strand	120-125	6	9
β-strand	128-130	3	9
β-strand	134-136	3	8
β-strand	140-141	2	8
β-strand	147-155	9	8
β-strand	165-168	4	9

Chain D: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	-24--18	7
β-strand	8-19	12	7
β-strand	24-33	10	7
β-strand	36-42	7	7
β-strand	48-50	3	7
α-helix	53-55	3
α-helix	56-65	10
α-helix	69-75	7
α-helix	76-81	6
α-helix	82-83	2
α-helix	84-88	5
α-helix	92-94	3
β-strand	98	1	10
α-helix	99-100	2
β-strand	101-106	6	11
β-strand	118-125	8	11
β-strand	126	1	10
β-strand	131-134	4	12
β-strand	145-147	3	11
α-helix	148-150	3
β-strand	151-152	2	11
β-strand	158-164	7	11
β-strand	176-179	4	12
β-strand	187-189	3	12

Chain E: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-17	12	13
β-strand	21-28	8	13
β-strand	31-37	7	13
β-strand	42-45	4	13
α-helix	59-78	20
α-helix	82-87	6
β-strand	90-95	6	14
β-strand	105-114	10	14
β-strand	120-125	6	15
β-strand	129	1	15
β-strand	134-136	3	14
β-strand	140-141	2	14
β-strand	147-155	9	14
β-strand	163-168	6	15

Chain F: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	-24--22	3
α-helix	-20--17	4
β-strand	8-19	12	13
β-strand	24-33	10	13
β-strand	36-42	7	13
β-strand	48-50	3	13
α-helix	53-55	3
α-helix	56-75	18
α-helix	76-81	6
α-helix	82-83	2
α-helix	84-88	5
α-helix	92-94	3
β-strand	98	1	16
β-strand	101-106	6	17
β-strand	116-125	10	17
β-strand	126	1	16
β-strand	131-136	6	18
β-strand	139-140	2	18
β-strand	145-147	3	17
α-helix	148-150	3
β-strand	151-152	2	17
β-strand	158-166	9	17
β-strand	174-179	6	18
β-strand	187-190	4	18

Chain G: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-17	12	19
β-strand	21-28	8	19
β-strand	31-37	7	19
β-strand	42-45	4	19
α-helix	50-53	4
α-helix	59-78	20
α-helix	83-86	4
β-strand	90-95	6	20
β-strand	105-114	10	20
β-strand	120-125	6	21
β-strand	128-130	3	21
β-strand	134-136	3	20
β-strand	140-141	2	20
β-strand	147-155	9	20
β-strand	163-168	6	21

Chain H: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	-24--17	8
β-strand	8-19	12	19
β-strand	24-33	10	19
β-strand	36-42	7	19
β-strand	47-50	4	19
α-helix	53-55	3
α-helix	56-65	10
α-helix	69-75	7
α-helix	76-81	6
α-helix	82	1
α-helix	83-88	6
α-helix	92-94	3
β-strand	98	1	22
β-strand	101-106	6	5
β-strand	116-125	10	5
β-strand	126	1	22
β-strand	131-136	6	23
β-strand	139-140	2	23
β-strand	145-148	4	5
α-helix	149-150	2
β-strand	151-152	2	5
β-strand	158-166	9	5
β-strand	174-179	6	23
β-strand	187-190	4	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class II histocompatibility antigen, A-D alpha chain	A, C, E, G	protein	173	Mus musculus	P04228 (AlphaFold model)
beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein	B, D, F, H	protein	212	Mus musculus	P26339 (AlphaFold model), Q31135 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>5DMK_1 H-2 class II histocompatibility antigen, A-D alpha chain (chains A, C, E, G)
DIEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEPQG
GLQNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVIN
ITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLE

Sequence of entity 2 (B, D, F, H), FASTA

>5DMK_2 beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein (chains B, D, F, H)
SRLGLWSRMDQLAKELTAELVPRGSGSERHFVHQFKGECYFTNGTQRIRLVTRYIYNREE
YLRFDSDVGEYRAVTELGRHSAEYYNKQYLERTRAELDTACRHNYEETEVPTSLRRLEQP
NVAISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQV
LVMLEMTPHQGEVYTCHVEHPSLKSPITVEWR

Ligands and cofactors

ID	Name	Formula	Copies
FLC	Citrate anion	C6 H5 O7	2

Primary citation

N-terminal additions to the WE14 peptide of chromogranin A create strong autoantigen agonists in type 1 diabetes. Jin, N., Wang, Y., Crawford, F. et al. Proc Natl Acad Sci U S A (2015) 112:13318-13323. DOI 10.1073/pnas.1517862112 · 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
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…
1F3J 3.1 Å, Histocompatibility antigen I-AG7

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