5UJT: Human HLA-DQ8

Crystal structure of human HLA-DQ8 in complex with insulin mimotope binding in register 3. Determined by X-ray diffraction at 1.94 Å resolution. Released 20 Dec 2017.

Method: X-ray diffraction
Resolution: 1.94 Å
Organism: Homo sapiens
Chains: 9
Atoms: 10,035
Mol. weight: 136.19 kDa
Ligands: NAG
Released: 20 Dec 2017

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

Secondary structure: helices and β-sheets

5UJT contains 37 α-helices and 84 β-strands across 9 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: 5 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	80-85	6
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-123	6	3
β-strand	126-127	2	3
α-helix	128	1
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	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-88	8
α-helix	90-92	3
β-strand	95	1	4
α-helix	96-97	2
β-strand	98-103	6	5
β-strand	113-122	10	5
β-strand	123	1	4
β-strand	128-133	6	6
β-strand	136-137	2	6
β-strand	142-144	3	5
α-helix	145-147	3
β-strand	148-149	2	5
β-strand	155-163	9	5
β-strand	170-176	7	6
β-strand	184-189	6	6

Chains C, F and I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4

Chain D: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	7
β-strand	19-26	8	7
β-strand	29-35	7	7
β-strand	40-43	4	7
α-helix	46-51	6
α-helix	56-76	21
α-helix	80-87	8
β-strand	88-93	6	8
β-strand	103-112	10	8
β-strand	118-123	6	9
β-strand	126-128	3	9
β-strand	132-134	3	8
α-helix	137	1
β-strand	138-139	2	8
β-strand	145-153	9	8
β-strand	161-166	6	9
β-strand	174-177	4	9

Chain E: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	7
β-strand	23-32	10	7
β-strand	35-41	7	7
β-strand	47-49	3	7
α-helix	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-88	8
α-helix	90-92	3
β-strand	95	1	10
α-helix	96-97	2
β-strand	98-103	6	11
β-strand	113-122	10	11
β-strand	123	1	10
β-strand	128-133	6	12
β-strand	136-137	2	12
β-strand	142-144	3	11
α-helix	145-147	3
β-strand	148-149	2	11
β-strand	155-163	9	11
β-strand	170-176	7	12
β-strand	184-189	6	12

Chain G: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	13
β-strand	19-26	8	13
β-strand	29-35	7	13
β-strand	40-43	4	13
α-helix	46-51	6
α-helix	56-76	21
α-helix	81-85	5
β-strand	88-93	6	14
β-strand	103-112	10	14
β-strand	118-123	6	15
β-strand	126-128	3	15
β-strand	132-134	3	14
α-helix	137	1
β-strand	138-139	2	14
β-strand	145-153	9	14
β-strand	161-166	6	15
β-strand	174-177	4	15

Chain H: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	13
β-strand	23-32	10	13
β-strand	35-41	7	13
β-strand	47-49	3	13
α-helix	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-88	8
α-helix	90-92	3
β-strand	95	1	16
α-helix	96-97	2
β-strand	98-102	5	17
β-strand	114-122	9	17
β-strand	123	1	16
β-strand	128-133	6	18
β-strand	137	1	18
β-strand	142-144	3	17
α-helix	145-147	3
β-strand	148-149	2	17
β-strand	155-162	8	17
β-strand	170-176	7	18
β-strand	184-189	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class II antigen	A, D, G	protein	185	Homo sapiens	Q5Y7C3 (AlphaFold model)
MHC class II HLA-DQ-beta-1	B, E, H	protein	189	Homo sapiens	O19707 (AlphaFold model)
insulin mimotope	C, F, I	protein	16	Homo sapiens

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

>5UJT_1 MHC class II antigen (chains A, D, G)
GEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDP
QFALTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPV
VNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLK
HWEPE

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

>5UJT_2 MHC class II HLA-DQ-beta-1 (chains B, E, H)
SPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEYWN
SQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDF
YPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQN
PIIVEWRAQ

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

>5UJT_3 insulin mimotope (chains C, F, I)
GVEELYLVAGEEGCGG

Ligands and cofactors

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

Primary citation

C-terminal modification of the insulin B:11-23 peptide creates superagonists in mouse and human type 1 diabetes. Wang, Y., Sosinowski, T., Novikov, A. et al. Proc Natl Acad Sci U S A (2018) 115:162-167. DOI 10.1073/pnas.1716527115 · PubMed

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