8W83: HLA-DQ2.5-alpha1 gliadin peptide

HLA-DQ2.5-alpha1 gliadin peptide in complex with DQN0344AE02. Determined by X-ray diffraction at 2.82 Å resolution. Released 8 Nov 2023.

Method: X-ray diffraction
Resolution: 2.82 Å
Organism: Homo sapiens
Chains: 16
Atoms: 23,643
Mol. weight: 382.1 kDa
Ligands: NAG
Released: 8 Nov 2023

Explore 8W83 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8W83 contains 91 α-helices and 299 β-strands across 16 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, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	34-40	7	3
β-strand	46-53	8	3
β-strand	59-61	3	3
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-100	8	3
α-helix	102-104	3
β-strand	112-113	2	3
β-strand	114	1	1
β-strand	117-119	3	3
β-strand	120-121	2	2
β-strand	127	1	4
β-strand	130-134	5	5
β-strand	145-155	11	5
β-strand	156	1	4
β-strand	161-164	4	6
α-helix	165-167	3
β-strand	169	1	6
β-strand	173-175	3	5
α-helix	176-178	3
β-strand	179-180	2	5
β-strand	186-195	10	5
α-helix	198-201	4
β-strand	205-210	6	6
β-strand	215-220	6	6

Chain B: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	7
β-strand	10-13	4	8
β-strand	19-24	6	7
β-strand	34-38	5	8
α-helix	43-44	2
β-strand	45-46	2	8
β-strand	48-49	2	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	8
β-strand	98-99	2	8
β-strand	103-107	5	8
β-strand	112	1	10
β-strand	115-119	5	11
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	11
β-strand	141	1	10
β-strand	145-151	7	12
β-strand	155	1	12
β-strand	160-161	2	11
β-strand	164	1	11
α-helix	165-168	4
β-strand	174-183	10	11
α-helix	184-187	4
β-strand	192-199	8	12
β-strand	206-211	6	12

Chain C: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	13
β-strand	22-29	8	13
β-strand	32-38	7	13
β-strand	43-46	4	13
α-helix	50-53	4
α-helix	59-78	20
α-helix	83-89	7
β-strand	90-95	6	14
β-strand	105-114	10	14
β-strand	120-125	6	15
β-strand	129-130	2	15
β-strand	134-136	3	14
α-helix	137-138	2
β-strand	140-141	2	14
β-strand	147-155	9	14
β-strand	163-168	6	15
β-strand	176-180	5	15

Chain D: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
β-strand	1008-1018	11	13
β-strand	1023-1032	10	13
β-strand	1035-1041	7	13
β-strand	1046-1049	4	13
α-helix	1052-1054	3
α-helix	1055-1063	9
α-helix	1065-1072	8
α-helix	1074	1
α-helix	1075-1079	5
α-helix	1080-1089	10
β-strand	1095	1	16
β-strand	1098-1103	6	17
β-strand	1115-1120	6	17
β-strand	1123	1	16
β-strand	1128-1132	5	18
β-strand	1138	1	18
α-helix	1139	1
β-strand	1142-1144	3	17
β-strand	1148-1149	2	17
β-strand	1155-1161	7	17
β-strand	1172-1176	5	18
β-strand	1184-1186	3	18

Chain E: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	18-25	8	19
β-strand	34-40	7	21
β-strand	47-53	7	21
β-strand	59-61	3	21
β-strand	69-74	6	19
β-strand	79-84	6	19
α-helix	89-91	3
β-strand	93-100	8	21
α-helix	102-104	3
β-strand	112-113	2	21
β-strand	114	1	19
β-strand	117-119	3	21
β-strand	120-121	2	20
β-strand	127	1	22
α-helix	128-129	2
β-strand	130-134	5	23
β-strand	146-155	10	23
β-strand	156	1	22
β-strand	161-164	4	24
β-strand	173-175	3	23
α-helix	176-178	3
β-strand	179-180	2	23
β-strand	186-194	9	23
β-strand	205-210	6	24
β-strand	215-220	6	24

Chain F: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	25
β-strand	10-13	4	26
β-strand	19-24	6	25
β-strand	33-38	6	27
β-strand	45-49	5	27
β-strand	53-54	2	27
α-helix	55	1
β-strand	62-65	4	25
β-strand	70-75	6	25
β-strand	85-90	6	27
β-strand	98-99	2	27
β-strand	103	1	27
β-strand	104-107	4	26
α-helix	108	1
β-strand	116-119	4	28
α-helix	123-126	4
β-strand	134-137	4	28
β-strand	146-151	6	29
β-strand	154-155	2	29
β-strand	161-165	5	28
α-helix	166-168	3
β-strand	175-179	5	28
β-strand	192-198	7	29
β-strand	206-211	6	29

Chain G: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	30
β-strand	23-29	7	30
β-strand	32-38	7	30
β-strand	43-46	4	30
α-helix	50-53	4
α-helix	59-78	20
α-helix	83-85	3
β-strand	87	1	31
α-helix	88-89	2
β-strand	90-95	6	32
β-strand	105-114	10	32
β-strand	115	1	31
β-strand	120-125	6	33
β-strand	128-130	3	33
β-strand	134-136	3	32
β-strand	140-141	2	32
β-strand	147-155	9	32
β-strand	163-168	6	33
β-strand	176-180	5	33

Chain H: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
β-strand	1008-1018	11	30
β-strand	1023-1032	10	30
β-strand	1035-1039	5	30
β-strand	1041	1	30
β-strand	1048-1049	2	30
α-helix	1052-1054	3
α-helix	1055-1061	7
α-helix	1065-1072	8
α-helix	1074	1
α-helix	1075-1079	5
α-helix	1080-1086	7
β-strand	1095	1	34
β-strand	1098-1102	5	35
β-strand	1116-1122	7	35
β-strand	1123	1	34
β-strand	1128-1132	5	36
β-strand	1137-1138	2	36
β-strand	1142-1144	3	35
β-strand	1148-1149	2	35
β-strand	1155-1161	7	35
β-strand	1172-1176	5	36
β-strand	1184	1	36

8 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
DQN0344AE02 Fab heavy chain	A, E, I, M	protein	228	Homo sapiens
DQN0344AE02 Fab light chain	B, F, J, N	protein	215	Homo sapiens
HLA class II histocompatibility antigen, DQ alpha 1 chain	C, G, K, O	protein	189	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein	D, H, L, P	protein	226	Homo sapiens	O19712 (AlphaFold model)

Sequence of entity 1 (A, E, I, M), FASTA

>8W83_1 DQN0344AE02 Fab heavy chain (chains A, E, I, M)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSSYWMCWVRQAPGQGLEWMGCVYGGSDTTY
YASWTKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDPLNYYYYGELNLWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 2 (B, F, J, N), FASTA

>8W83_2 DQN0344AE02 Fab light chain (chains B, F, J, N)
DIQMTQSPSSLSASVGDRVTITCQATENIYSGLAWYQQKPGKAPKLLIYYVSTLASGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQTYHDISEVTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, G, K, O), FASTA

>8W83_3 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains C, G, K, O)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWSLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPELEVLFQ

Sequence of entity 4 (D, H, L, P), FASTA

>8W83_4 MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein (chains D, H, L, P)
QLQPFPQPELPYPGSGGGGSIEGRGSGGGSRDSPEDFVYQFKGMCYFTNGTERVRLVSRS
IYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTT
LQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRN
GDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRALEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Characterizations of a neutralizing antibody broadly reactive to multiple gluten peptide:HLA-DQ2.5 complexes in the context of celiac disease. Okura, Y., Ikawa-Teranishi, Y., Mizoroki, A. et al. Nat Commun (2023) 14:8502-8502. DOI 10.1038/s41467-023-44083-4 · 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
1JK8 2.4 Å, Crystal structure of a human insulin peptide-HLA-DQ8 complex
6XP6 2.4 Å, 3C11-DQ2-glia-a2 complex
9EJH 2.45 Å, Peptide-independent T cell receptor recognition of HLA-DQ2

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