8W84: HLA-DQ2.5-alpha2 gliadin peptide

HLA-DQ2.5-alpha2 gliadin peptide in complex with DQN0344AE02. Determined by X-ray diffraction at 2.1 Å resolution. Released 8 Nov 2023.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,415
Mol. weight: 95.73 kDa
Ligands: NAG
Released: 8 Nov 2023

Explore 8W84 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8W84 contains 29 α-helices and 79 β-strands across 4 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: 9 helices, 23 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
α-helix	63-65	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	117-119	3	3
β-strand	120-121	2	2
α-helix	124-126	3
β-strand	127	1	4
α-helix	128-129	2
β-strand	130-134	5	5
β-strand	146-155	10	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	186-194	9	5
α-helix	196-198	3
β-strand	205-210	6	6
α-helix	211-213	3
β-strand	215-220	6	6

Chain B: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
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	9
α-helix	113-116	4
β-strand	117-119	3	10
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-136	7	10
β-strand	140	1	11
β-strand	141	1	9
β-strand	145-151	7	12
β-strand	154-155	2	12
α-helix	156	1
β-strand	164	1	13
β-strand	174	1	11
β-strand	176	1	13
β-strand	179-183	5	10
α-helix	184-187	4
β-strand	192-199	8	12
β-strand	206-211	6	12

Chain C: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	7-17	11	14
β-strand	22-29	8	14
β-strand	32-38	7	14
β-strand	43-46	4	14
α-helix	49-53	5
α-helix	58-78	21
α-helix	83-86	4
β-strand	87	1	15
β-strand	90-95	6	16
β-strand	100	1	17
β-strand	103	1	17
β-strand	105-114	10	16
β-strand	115	1	15
β-strand	120-125	6	18
β-strand	128-129	2	18
β-strand	134-136	3	16
α-helix	139	1
β-strand	140-141	2	16
β-strand	147-155	9	16
β-strand	163-168	6	18
β-strand	176-179	4	18

Chain D: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	1008-1018	11	14
β-strand	1023-1032	10	14
β-strand	1035-1041	7	14
β-strand	1046-1049	4	14
α-helix	1052-1054	3
α-helix	1055-1062	8
α-helix	1065-1074	10
α-helix	1075-1080	6
α-helix	1081-1087	7
α-helix	1090-1092	3
β-strand	1095	1	19
β-strand	1098-1103	6	20
β-strand	1114-1122	9	20
β-strand	1123	1	19
β-strand	1128-1133	6	21
β-strand	1136-1138	3	21
β-strand	1142-1144	3	20
α-helix	1145-1147	3
β-strand	1148-1149	2	20
β-strand	1155-1162	8	20
β-strand	1170-1176	7	21
β-strand	1184-1189	6	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DQN0344AE02 Fab heavy chain	A	protein	228	Homo sapiens
DQN0344AE02 Fab light chain	B	protein	215	Homo sapiens
HLA class II histocompatibility antigen, DQ alpha 1 chain	C	protein	189	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ-beta-1 - alpha2 gliadin peptide chimeric protein	D	protein	226	Homo sapiens	O19712 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8W84_1 DQN0344AE02 Fab heavy chain (chains A)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSSYWMCWVRQAPGQGLEWMGCVYGGSDTTY
YASWTKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDPLNYYYYGELNLWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 2 (B), FASTA

>8W84_2 DQN0344AE02 Fab light chain (chains B)
DIQMTQSPSSLSASVGDRVTITCQATENIYSGLAWYQQKPGKAPKLLIYYVSTLASGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQTYHDISEVTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C), FASTA

>8W84_3 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains C)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWSLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPELEVLFQ

Sequence of entity 4 (D), FASTA

>8W84_4 MHC class II HLA-DQ-beta-1 - alpha2 gliadin peptide chimeric protein (chains D)
LPYPQPELPYPQPGSGGGGSIEGRGSGGGSRDSPEDFVYQFKGMCYFTNGTERVRLVSRS
IYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTT
LQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRN
GDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRALEVLFQ

Ligands and cofactors

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

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
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
6MFF 2.6 Å, HLA-DQ2-glia-omega1

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