8VDU: Hybrid insulin peptide

Crystal structure of hybrid insulin peptide (InsC8-15-IAPP74-80) bound to HLA-DQ8. Determined by X-ray diffraction at 3.5 Å resolution. Released 7 Aug 2024.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 12
Atoms: 12,192
Mol. weight: 182.22 kDa
Ligands: NAG
Released: 7 Aug 2024

Explore 8VDU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VDU contains 43 α-helices and 120 β-strands across 12 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: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	1
β-strand	20-26	7	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-51	6
β-strand	54	1	2
α-helix	57-76	20
α-helix	81-87	7
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	117-123	7	4
β-strand	126-127	2	4
α-helix	128	1
β-strand	132-134	3	3
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-167	7	4
β-strand	174-178	5	4

Chain B: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
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	65-72	8
α-helix	74	1
α-helix	75-79	5
α-helix	80-86	7
α-helix	90-92	3
β-strand	95	1	5
β-strand	98-103	6	6
β-strand	115-122	8	6
β-strand	123	1	5
β-strand	128-133	6	7
β-strand	136-137	2	7
β-strand	142-144	3	6
α-helix	145-147	3
β-strand	148-149	2	6
β-strand	155-161	7	6
β-strand	170-176	7	7
β-strand	184-189	6	7

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	2
α-helix	6-11	6

Chain D: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	8
β-strand	19-26	8	8
β-strand	29-35	7	8
β-strand	40-43	4	8
α-helix	46-51	6
β-strand	53	1	9
α-helix	57-76	20
α-helix	81-87	7
β-strand	88-93	6	10
β-strand	103-112	10	10
β-strand	118-123	6	11
β-strand	126-127	2	11
α-helix	128	1
β-strand	132-134	3	10
β-strand	138-139	2	10
β-strand	145-153	9	10
β-strand	161-166	6	11
β-strand	174-178	5	11

Chain E: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	8
β-strand	23-32	10	8
β-strand	35-41	7	8
β-strand	47-49	3	8
α-helix	55-63	9
α-helix	65-72	8
α-helix	74	1
α-helix	75-79	5
α-helix	80-86	7
β-strand	95	1	12
β-strand	99-103	5	13
β-strand	113-122	10	13
β-strand	123	1	12
β-strand	128-133	6	14
β-strand	136-137	2	14
β-strand	142-144	3	13
α-helix	145-147	3
β-strand	148-149	2	13
β-strand	155-163	9	13
β-strand	170-176	7	14
β-strand	184-189	6	14

Chain F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	9
α-helix	7-12	6

Chain G: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	15
β-strand	20-26	7	15
β-strand	29-35	7	15
β-strand	40-43	4	15
α-helix	46-51	6
β-strand	53-54	2	16
α-helix	57-76	20
α-helix	81-87	7
β-strand	88-93	6	17
β-strand	103-112	10	17
β-strand	118-123	6	18
β-strand	126-128	3	18
β-strand	132-134	3	17
β-strand	138-139	2	17
β-strand	145-153	9	17
β-strand	161-166	6	18
β-strand	174-178	5	18

Chains H and K: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	15
β-strand	23-32	10	15
β-strand	35-41	7	15
β-strand	47-49	3	15
α-helix	55-63	9
α-helix	65-72	8
α-helix	74	1
α-helix	75-79	5
α-helix	80-86	7
β-strand	95	1	19
β-strand	98-103	6	20
β-strand	113-122	10	20
β-strand	123	1	19
β-strand	128-133	6	21
β-strand	136-137	2	21
β-strand	142-144	3	20
α-helix	145-147	3
β-strand	148-149	2	20
β-strand	155-163	9	20
β-strand	170-176	7	21
β-strand	184-189	6	21

3 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
MHC class II HLA-DQ-alpha chain	A, D, G, J	protein	185	Homo sapiens	Q30069 (AlphaFold model)
MHC class II HLA-DQ-beta-1	B, E, H, K	protein	192	Homo sapiens	O19707 (AlphaFold model)
Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80)	C, F, I, L	protein	15	Homo sapiens

Sequence of entity 1 (A, D, G, J), FASTA

>8VDU_1 MHC class II HLA-DQ-alpha chain (chains A, D, G, J)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPES

Sequence of entity 2 (B, E, H, K), FASTA

>8VDU_2 MHC class II HLA-DQ-beta-1 (chains B, E, H, K)
RDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEY
WNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVT
DFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSL
QNPIIVEWRAQS

Sequence of entity 3 (C, F, I, L), FASTA

>8VDU_3 Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80) (chains C, F, I, L)
GQVELGGGNAVEVCK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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

Primary citation

A structural basis of T cell cross-reactivity to native and spliced self-antigens presented by HLA-DQ8. Tran, M.T., Lim, J.J., Loh, T.J. et al. J Biol Chem (2024) 300:107612-107612. DOI 10.1016/j.jbc.2024.107612 · PubMed

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

6DFX 2.03 Å, human diabetogenic TCR T1D3 in complex with DQ8-p8E9E peptide
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

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