7SG0: W316 TCR

W316 TCR in complex with HLA-DQ2-omega1. Determined by X-ray diffraction at 3.0 Å resolution. Released 23 Feb 2022.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,449
Mol. weight: 96.14 kDa
Ligands: NAG
Released: 23 Feb 2022

Explore 7SG0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SG0 contains 21 α-helices and 73 β-strands across 5 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: 3 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	46-50	5
α-helix	56-76	21
α-helix	81-84	4
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-123	6	3
β-strand	126-128	3	3
β-strand	132-134	3	2
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: 8 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	52-54	3
α-helix	55-61	7
α-helix	65-72	8
α-helix	74	1
α-helix	75-79	5
α-helix	80-86	7
β-strand	95	1	4
α-helix	96-97	2
β-strand	98-102	5	5
β-strand	114-122	9	5
β-strand	123	1	4
β-strand	128-133	6	6
β-strand	137	1	6
β-strand	144	1	5
α-helix	145-147	3
β-strand	148-149	2	5
β-strand	155-162	8	5
β-strand	171-176	6	6
β-strand	184-188	5	6

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5

Chain D: 1 helix, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	11-14	4	8
β-strand	19-21	3	9
β-strand	23-26	4	7
β-strand	37-44	8	10
β-strand	50-56	7	10
β-strand	67-68	2	9
β-strand	76-78	3	9
β-strand	81	1	7
β-strand	86	1	7
β-strand	89-91	3	9
α-helix	96-98	3
β-strand	101-108	8	10
β-strand	122-123	2	10
β-strand	124-127	4	8
β-strand	136-139	4	11
β-strand	141-142	2	12
β-strand	149-154	6	11
β-strand	171-172	2	11
β-strand	176-180	5	11
β-strand	185-194	10	11
β-strand	215	1	11

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	13
β-strand	10-14	5	14
β-strand	19-23	5	13
α-helix	25-26	2
β-strand	38-44	7	14
β-strand	51-57	7	14
β-strand	64-67	4	14
β-strand	76-79	4	13
α-helix	81-84	3
β-strand	87-91	5	13
α-helix	96-98	3
β-strand	101-107	7	14
β-strand	117-118	2	14
β-strand	122-127	6	14
α-helix	130-132	3
β-strand	134	1	15
β-strand	137-142	6	12
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	12
β-strand	164	1	15
β-strand	168-174	7	16
β-strand	177-179	3	16
β-strand	183-185	3	12
β-strand	190-191	2	12
β-strand	201-210	10	12
α-helix	211-214	4
β-strand	220-227	8	16
β-strand	230	1	17
α-helix	241-242	2
β-strand	244	1	17
β-strand	246-253	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DQ alpha 1 chain	A	protein	183	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ-beta-1	B	protein	207	Homo sapiens	O19712 (AlphaFold model)
DQ2-glia-omega1 peptide	C	protein	11	Homo sapiens
T-cell receptor, w316, alpha chain	D	protein	208	Homo sapiens
T-cell receptor, w316, beta chain	E	protein	240	Homo sapiens

Sequence of entity 1 (A), FASTA

>7SG0_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPE

Sequence of entity 2 (B), FASTA

>7SG0_2 MHC class II HLA-DQ-beta-1 (chains B)
GSGGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVG
EFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSR
TEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTP
QRGDVYTCHVEHPSLQSPITVEWRAQS

Sequence of entity 3 (C), FASTA

>7SG0_3 DQ2-glia-omega1 peptide (chains C)
QPFPQPEQPFP

Sequence of entity 4 (D), FASTA

>7SG0_4 T-cell receptor, w316, alpha chain (chains D)
HMNSVTQMEGPVTLSEEAFLTINCTYTATGYPSLFWYVQYPGEGLQLLLKATKADDKGSN
KGFEATYRKETTSFHLEKGSVQVSDSAVYFCALSGGTSYGKLTFGQGTILTVHPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>7SG0_5 T-cell receptor, w316, beta chain (chains E)
HMQTPSNKVTEKGKYVELRCDPISGHTALYWYRQSLGQGPEFLIYFQGTGAADDSGLPND
RFFAVRPEGSVSTLKIQRTERGDSAVYLCASSQGQDTEAFFGQGTRLTVVEDLNKVFPPE
VAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Ligands and cofactors

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

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structural basis of T cell receptor specificity and cross-reactivity of two HLA-DQ2.5-restricted gluten epitopes in celiac disease. Ciacchi, L., Farenc, C., Dahal-Koirala, S. et al. J Biol Chem (2022) 298:101619-101619. DOI 10.1016/j.jbc.2022.101619 · 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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