7SG1: XPA5 TCR

XPA5 TCR in complex with HLA-DQ2-alpha1. Determined by X-ray diffraction at 3.1 Å resolution. Released 23 Feb 2022.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,544
Mol. weight: 194.95 kDa
Ligands: NAG, CA
Released: 23 Feb 2022

Explore 7SG1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SG1 contains 42 α-helices and 133 β-strands across 9 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, 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	46-48	3
α-helix	56-76	21
α-helix	81-83	3
α-helix	85-87	3
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	133-134	2	2
α-helix	135-137	3
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	46-49	4	1
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
α-helix	90-92	3
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	142-144	3	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	184-187	4	6

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5

Chain D: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	13
β-strand	10-14	5	14
β-strand	19-24	6	13
β-strand	38-44	7	14
β-strand	50-56	7	14
β-strand	66-67	2	13
β-strand	77-79	3	13
β-strand	86-91	6	13
α-helix	96-98	3
β-strand	100-107	8	14
β-strand	122-127	6	14
α-helix	128	1
β-strand	136-140	5	15
β-strand	150-154	5	15
β-strand	171-172	2	15
β-strand	176-180	5	15
α-helix	181-183	3
β-strand	185-193	9	15
β-strand	215	1	15

Chain E: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	16
β-strand	10-14	5	17
β-strand	19-25	7	16
β-strand	38-44	7	17
β-strand	50-56	7	17
α-helix	64-65	2
β-strand	66-67	2	17
β-strand	78-83	5	16
β-strand	86-91	6	16
α-helix	96-98	3
β-strand	100-107	8	17
α-helix	116	1
β-strand	117-118	2	17
β-strand	122-127	6	17
β-strand	137-141	5	18
α-helix	142-144	3
α-helix	145-150	6
β-strand	153-163	11	18
β-strand	168-174	7	19
β-strand	177-179	3	19
β-strand	183-185	3	18
α-helix	189	1
β-strand	190-191	2	18
β-strand	201-210	10	18
α-helix	211-214	4
β-strand	220-227	8	19
β-strand	230	1	20
α-helix	241-242	2
β-strand	244	1	20
β-strand	246-253	8	19

Chain F: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	7
β-strand	19-26	8	7
β-strand	29-35	7	7
β-strand	40-43	4	7
α-helix	46-48	3
α-helix	56-76	21
α-helix	85-87	3
β-strand	88-93	6	8
β-strand	103-112	10	8
β-strand	118-122	5	9
β-strand	127-128	2	9
β-strand	132-134	3	8
β-strand	138-139	2	8
β-strand	145-153	9	8
β-strand	161-166	6	9
β-strand	174-178	5	9

Chain G: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	7
β-strand	23-32	10	7
β-strand	35-41	7	7
β-strand	46-49	4	7
α-helix	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
α-helix	90-92	3
β-strand	95	1	10
β-strand	98-102	5	11
β-strand	114-122	9	11
β-strand	123	1	10
β-strand	128-133	6	12
β-strand	137	1	12
β-strand	142-144	3	11
α-helix	145-147	3
β-strand	148-149	2	11
β-strand	155-162	8	11
β-strand	170-176	7	12
β-strand	184-189	6	12

Chain I: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	21
β-strand	10-14	5	22
β-strand	19-24	6	21
β-strand	38-44	7	22
β-strand	52-56	5	22
β-strand	66-67	2	21
β-strand	77-79	3	21
β-strand	86-91	6	21
α-helix	96-98	3
β-strand	100-107	8	22
β-strand	122-127	6	22
β-strand	136-137	2	23
β-strand	151-154	4	23
β-strand	178-180	3	24
β-strand	185-187	3	24
β-strand	189-192	4	23

1 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
HLA class II histocompatibility antigen, DQ alpha 1 chain	A, F	protein	183	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ-beta-1	B, G	protein	202	Homo sapiens	Q5Y7D3 (AlphaFold model)
T-cell receptor, xpa5, alpha chain	D, I	protein	203	Homo sapiens
T-cell receptor, xpa5, beta chain	E, J	protein	259	Homo sapiens
DQ2-glia-alpha1a peptide	C, H	protein	16	Homo sapiens

Sequence of entity 1 (A, F), FASTA

>7SG1_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A, F)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPE

Sequence of entity 2 (B, G), FASTA

>7SG1_2 MHC class II HLA-DQ-beta-1 (chains B, G)
IEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAV
TLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALN
HHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDV
YTCHVEHPSLQSPITVEWRAQS

Sequence of entity 3 (D, I), FASTA

>7SG1_3 T-cell receptor, xpa5, alpha chain (chains D, I)
HMKTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEVA
SLFIPADRKSSTLSLPRVSLSDTAVYYCLVGGLARDMRFGAGTRLTVKPNIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E, J), FASTA

>7SG1_4 T-cell receptor, xpa5, beta chain (chains E, J)
SIEGRGGSGASRDHMAVISQKPSRDICQRGTSLTIQCQVDSQVTMMFWYRQQPGQSLTLI
ATANQGSEATYESGFVIDKFPISRPNLTFSTLTVSNMSPEDSSIYLCSVALGSDTGELFF
GEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKE
VHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQ
DRAKPVTQIVSAEAWGRAD

Sequence of entity 5 (C, H), FASTA

>7SG1_5 DQ2-glia-alpha1a peptide (chains C, H)
LQPFPQPELPYGSGGS

Ligands and cofactors

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