1JK8: Human insulin peptide-HLA-DQ8 complex

Crystal structure of a human insulin peptide-HLA-DQ8 complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 22 Aug 2001.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,198
Mol. weight: 44.72 kDa
Ligands: NAG
Released: 22 Aug 2001

Explore 1JK8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1JK8 contains 12 α-helices and 28 β-strands across 3 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-51	6
α-helix	56-76	21
α-helix	80-84	5
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-123	6	3
β-strand	126-128	3	3
β-strand	132-134	3	2
α-helix	137	1
β-strand	138-139	2	2
β-strand	145-153	9	2
β-strand	161-166	6	3
β-strand	174-178	5	3

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	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-87	7
α-helix	90-92	3
β-strand	95	1	4
α-helix	96-97	2
β-strand	98-103	6	5
β-strand	114-122	9	5
β-strand	123	1	4
β-strand	128-133	6	6
β-strand	136-138	3	6
β-strand	142-144	3	5
α-helix	145-147	3
β-strand	148-149	2	5
β-strand	155-162	8	5
β-strand	170-176	7	6
β-strand	184-189	6	6

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class II HLA-DQ8	A	protein	181	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ8	B	protein	190	Homo sapiens	P01920 (AlphaFold model)
insulin B peptide	C	protein	14	Homo sapiens	P01308 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1JK8_1 MHC class II HLA-DQ8 (chains A)
VADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFAL
TNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNIT
WLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEP
E

Sequence of entity 2 (B), FASTA

>1JK8_2 MHC class II HLA-DQ8 (chains B)
SPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEYWN
SQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDF
YPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQN
PIIVEWRAQS

Sequence of entity 3 (C), FASTA

>1JK8_3 insulin B peptide (chains C)
LVEALYLVCGERGG

Ligands and cofactors

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

Primary citation

Structure of a human insulin peptide-HLA-DQ8 complex and susceptibility to type 1 diabetes. Lee, K.H., Wucherpfennig, K.W., Wiley, D.C. Nat Immunol (2001) 2:501-507. DOI 10.1038/88694 · PubMed

Other PDB entries of the same protein (UniProt P01909 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6U3M 1.9 Å, DQ2-P.fluor-alpha1a
5KSA 2.0 Å, Bel602-DQ8.5-glia-gamma1 complex
6MFG 2.0 Å, HLA-DQ2-glia-alpha1
2NNA 2.1 Å, Structure of the MHC class II molecule HLA-DQ8 bound with a deamidated gluten peptide
8W84 2.1 Å, HLA-DQ2.5-alpha2 gliadin peptide in complex with DQN0344AE02
5KSV 2.19 Å, Crystal structure of HLA-DQ2.5-CLIP2
9EJG 2.2 Å, Peptide-independent T cell receptor recognition of HLA-DQ2
1S9V 2.22 Å, Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide
8W86 2.24 Å, HLA-DQ2.5-B/C hordein peptide in complex with DQN0385AE02
6XP6 2.4 Å, 3C11-DQ2-glia-a2 complex
9EJH 2.45 Å, Peptide-independent T cell receptor recognition of HLA-DQ2
6MFF 2.6 Å, HLA-DQ2-glia-omega1

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