8W86: HLA-DQ2.5-B/C hordein peptide

HLA-DQ2.5-B/C hordein peptide in complex with DQN0385AE02. Determined by X-ray diffraction at 2.24 Å resolution. Released 8 Nov 2023.

Method: X-ray diffraction
Resolution: 2.24 Å
Organism: Homo sapiens
Chains: 8
Atoms: 11,188
Mol. weight: 190.32 kDa
Ligands: NAG
Released: 8 Nov 2023

Explore 8W86 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8W86 contains 39 α-helices and 124 β-strands across 8 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, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-40	7	2
β-strand	47-53	7	2
β-strand	59-61	3	2
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-99	7	2
β-strand	108	1	2
β-strand	112-116	5	2
β-strand	122	1	3
β-strand	125-129	5	4
β-strand	141-150	10	4
β-strand	151	1	3
β-strand	156-157	2	5
β-strand	168-170	3	4
α-helix	171-173	3
β-strand	174-175	2	4
β-strand	181-189	9	4
β-strand	200-202	3	6
β-strand	203-204	2	5
β-strand	205	1	7
α-helix	206-208	3
β-strand	210	1	7
β-strand	213-215	3	6

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	34-38	5	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-90	7	9
β-strand	96-97	2	9
β-strand	101-106	6	9
β-strand	110	1	10
β-strand	113-117	5	11
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	11
β-strand	139	1	10
β-strand	144-149	6	12
β-strand	152-153	2	12
α-helix	154	1
β-strand	158-162	5	11
α-helix	163-166	4
β-strand	172-181	10	11
α-helix	182-186	5
β-strand	190-196	7	12
β-strand	204-209	6	12

Chain C: 3 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	49-53	5
α-helix	58-78	21
β-strand	90-95	6	14
β-strand	105-114	10	14
β-strand	120-125	6	15
β-strand	128-130	3	15
β-strand	134-136	3	14
α-helix	139	1
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: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	1-10	10
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	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	16
β-strand	1098-1103	6	17
β-strand	1114-1122	9	17
β-strand	1123	1	16
β-strand	1128-1133	6	18
β-strand	1136-1138	3	18
β-strand	1142-1144	3	17
α-helix	1145-1147	3
β-strand	1148-1149	2	17
β-strand	1155-1162	8	17
β-strand	1170-1176	7	18
β-strand	1184-1189	6	18

Chain E: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11	1	20
β-strand	18-25	8	19
α-helix	29-31	3
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	93-99	7	21
β-strand	108	1	21
β-strand	113-114	2	21
β-strand	115	1	20

Chain F: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	22
β-strand	10-13	4	23
β-strand	19-25	7	22
β-strand	34-38	5	23
β-strand	45-49	5	23
β-strand	53-54	2	23
α-helix	55	1
β-strand	62-67	6	22
β-strand	70-75	6	22
α-helix	80-82	3
β-strand	85-90	6	23
β-strand	96-97	2	23
β-strand	101-105	5	23

Chain G: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	24
β-strand	22-29	8	24
β-strand	32-38	7	24
β-strand	43-46	4	24
α-helix	49-53	5
α-helix	58-78	21
α-helix	83-87	5
β-strand	90-95	6	25
β-strand	105-114	10	25
β-strand	120-125	6	26
β-strand	128-129	2	26
α-helix	130	1
β-strand	134-136	3	25
α-helix	139	1
β-strand	140-141	2	25
β-strand	147-155	9	25
β-strand	163-168	6	26
β-strand	176-180	5	26

Chain H: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	1-4	4
α-helix	6-9	4
β-strand	1008-1018	11	24
β-strand	1023-1032	10	24
β-strand	1035-1041	7	24
β-strand	1047-1049	3	24
α-helix	1052-1054	3
α-helix	1055-1063	9
α-helix	1065-1074	10
α-helix	1075-1080	6
α-helix	1081-1088	8
α-helix	1090-1092	3
β-strand	1095	1	27
β-strand	1098-1103	6	28
β-strand	1114-1122	9	28
β-strand	1123	1	27
β-strand	1128-1133	6	29
β-strand	1136-1138	3	29
β-strand	1142-1144	3	28
α-helix	1145-1147	3
β-strand	1148-1149	2	28
β-strand	1155-1162	8	28
β-strand	1171-1176	6	29
β-strand	1184-1188	5	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DQN0385AE02 Fab heavy chain	A, E	protein	223	Homo sapiens
DQN0385AE02 Fab light chain	B, F	protein	213	Homo sapiens
HLA class II histocompatibility antigen, DQ alpha 1 chain	C, G	protein	189	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ-beta-1 - B/C hordein peptide chimeric protein	D, H	protein	230	Homo sapiens	O19712 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>8W86_1 DQN0385AE02 Fab heavy chain (chains A, E)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSEWYFMSWVRQAPGKGLEWVASIDTGSGSID
YAGWVEGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDIGIDYNFWGEGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVEDYFPEPVTVSWNSGALTSGVHTFPAVLESSGL
YSLSSVVTVPSSSLGTKTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 2 (B, F), FASTA

>8W86_2 DQN0385AE02 Fab light chain (chains B, F)
DIQMTQSPSSLSASVGDRVTITCQTTQEISSYLNWYQQKPGQPPKLLIYYASTKAEGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCHYGISKVSFGQGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTAKVVCLLNNFYPREAKVQWKVDNALQSGNSKESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, G), FASTA

>8W86_3 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains C, G)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWSLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPELEVLFQ

Sequence of entity 4 (D, H), FASTA

>8W86_4 MHC class II HLA-DQ-beta-1 - B/C hordein peptide chimeric protein (chains D, H)
EPEQPIPEQPQPYPQQPGSGGGGSIEGRGSGGGSRDSPEDFVYQFKGMCYFTNGTERVRL
VSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLE
LRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTP
LIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRALEVLFQ

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
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
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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