8W85: HLA-DQ2.5-gamma2 gliadin peptide

HLA-DQ2.5-gamma2 gliadin peptide in complex with DQN0385AE01. Determined by X-ray diffraction at 2.77 Å resolution. Released 8 Nov 2023.

Method: X-ray diffraction
Resolution: 2.77 Å
Organism: Homo sapiens
Chains: 8
Atoms: 10,295
Mol. weight: 188.17 kDa
Ligands: NAG
Released: 8 Nov 2023

Explore 8W85 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8W85 contains 33 α-helices and 120 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: 6 helices, 22 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	46-53	8	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	113-116	4	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	156-159	4	5
α-helix	160-162	3
β-strand	164	1	5
β-strand	168-170	3	4
α-helix	171-173	3
β-strand	174-175	2	4
β-strand	181-189	9	4
α-helix	193-196	4
β-strand	199-204	6	5
α-helix	206-208	3
β-strand	212-216	5	5

Chain B: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	34-38	5	7
α-helix	43-44	2
β-strand	45-48	4	7
β-strand	49	1	8
β-strand	52	1	8
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
β-strand	96-97	2	7
β-strand	101-105	5	7
α-helix	110-112	3
β-strand	113-117	5	9
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	9
β-strand	144-149	6	10
β-strand	152-154	3	10
β-strand	172-181	10	9
β-strand	190-196	7	10
β-strand	204-209	6	10

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	11
β-strand	22-29	8	11
β-strand	32-38	7	11
β-strand	43-46	4	11
α-helix	49-53	5
α-helix	58-78	21
α-helix	83-87	5
β-strand	90-95	6	12
β-strand	105-114	10	12
β-strand	121-125	5	13
β-strand	128-130	3	13
β-strand	134-136	3	12
β-strand	147-155	9	12
β-strand	163-167	5	13
β-strand	176-180	5	13

Chain D: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
β-strand	1008-1018	11	11
β-strand	1023-1032	10	11
β-strand	1035-1041	7	11
β-strand	1047-1049	3	11
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
β-strand	1095	1	14
β-strand	1098-1103	6	15
β-strand	1115-1122	8	15
β-strand	1123	1	14
β-strand	1128-1130	3	16
β-strand	1142-1144	3	15
α-helix	1145-1147	3
β-strand	1148-1149	2	15
β-strand	1155-1161	7	15
β-strand	1172-1176	5	16
β-strand	1184-1187	4	16

Chain E: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	17
β-strand	10-12	3	18
β-strand	18-20	3	19
β-strand	21	1	17
β-strand	34-40	7	18
β-strand	46-53	8	18
β-strand	59-61	3	18
β-strand	69-74	6	19
β-strand	79-84	6	19
α-helix	89-91	3
β-strand	93-99	7	18
β-strand	108	1	18
β-strand	112-116	5	18
α-helix	123-125	3

Chain F: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	20
β-strand	10-12	3	21
α-helix	17-18	2
β-strand	19-25	7	20
β-strand	34-38	5	21
β-strand	45-46	2	21
β-strand	49	1	22
β-strand	52	1	22
β-strand	62-67	6	20
β-strand	70-75	6	20
β-strand	85-90	6	21
β-strand	96-97	2	21
β-strand	101-104	4	21

Chain G: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	23
β-strand	22-23	2	23
β-strand	25-29	5	23
β-strand	32-38	7	23
β-strand	43-46	4	23
α-helix	49-53	5
α-helix	58-78	21
α-helix	83-85	3
β-strand	90-95	6	24
β-strand	105-114	10	24
β-strand	120-123	4	25
β-strand	124-125	2	26
β-strand	128-129	2	26
β-strand	134-136	3	24
β-strand	140-141	2	24
β-strand	147-155	9	24
β-strand	164-168	5	25
β-strand	176-179	4	25

Chain H: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	1-6	6
β-strand	1008-1018	11	23
β-strand	1023-1032	10	23
β-strand	1035-1041	7	23
β-strand	1047-1049	3	23
α-helix	1055-1063	9
α-helix	1065-1074	10
α-helix	1075-1080	6
α-helix	1081-1087	7
β-strand	1095	1	27
β-strand	1098-1103	6	28
β-strand	1115-1122	8	28
β-strand	1123	1	27
β-strand	1128-1129	2	29
β-strand	1142-1144	3	28
α-helix	1145-1146	2
β-strand	1148-1149	2	28
β-strand	1155-1161	7	28
β-strand	1173-1176	4	29
β-strand	1184-1186	3	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DQN0385AE01 Fab heavy chain	A, E	protein	223	Homo sapiens
DQN0385AE01 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 - gamma2 gliadin peptide chimeric protein	D, H	protein	222	Homo sapiens	O19712 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>8W85_1 DQN0385AE01 Fab heavy chain (chains A, E)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSWYWICWVRQAPGKGLEWVACIDTGSGSID
YASWVNGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDIGIDYNFWGPGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 2 (B, F), FASTA

>8W85_2 DQN0385AE01 Fab light chain (chains B, F)
DIQMTQSPSSLSASVGDRVTITCQATQSISSYLNWYQQKPGQPPKLLIYYASTLAYGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCHYGISVVSFGQGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, G), FASTA

>8W85_3 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains C, G)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWSLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPELEVLFQ

Sequence of entity 4 (D, H), FASTA

>8W85_4 MHC class II HLA-DQ-beta-1 - gamma2 gliadin peptide chimeric protein (chains D, H)
IIQPEQPAQLPGGGGSIEGRGSGGGSRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNR
EEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRR
VEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWT
FQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRALEVLFQ

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
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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