7SG2: XPA5 TCR

XPA5 TCR in complex with HLA-DQ2-omega1. 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: 12,551
Mol. weight: 192.57 kDa
Ligands: CA, NAG
Released: 23 Feb 2022

Explore 7SG2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SG2 contains 43 α-helices and 133 β-strands across 10 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	85-87	3
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-123	6	3
β-strand	126-127	2	3
β-strand	132-134	3	2
β-strand	138-139	2	2
β-strand	145-153	9	2
β-strand	162-166	5	3
β-strand	174-177	4	3

Chain B: 7 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	55-63	9
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
α-helix	90-92	3
β-strand	95	1	4
β-strand	99-103	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
β-strand	148-149	2	5
β-strand	155-162	8	5
β-strand	170-176	7	6
β-strand	184-189	6	6

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1-5	5
α-helix	7-9	3

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
α-helix	113-115	3
β-strand	122-127	6	14
β-strand	136-142	7	15
β-strand	149-154	6	15
β-strand	171-172	2	15
α-helix	173-175	3
β-strand	176-180	5	15
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
β-strand	66-67	2	17
α-helix	68	1
β-strand	78-83	5	16
β-strand	86-91	6	16
β-strand	101-107	7	17
α-helix	115-116	2
β-strand	117-118	2	17
β-strand	122-127	6	17
α-helix	130-132	3
β-strand	137-142	6	15
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	15
β-strand	168-174	7	18
β-strand	177-179	3	18
β-strand	183-185	3	15
α-helix	189	1
β-strand	190-191	2	15
β-strand	201-210	10	15
α-helix	211-214	4
β-strand	220-227	8	18
β-strand	230	1	19
α-helix	241-242	2
β-strand	244	1	19
β-strand	246-253	8	18

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	46-50	5
α-helix	56-76	21
α-helix	85-87	3
β-strand	88-93	6	8
β-strand	103-112	10	8
β-strand	117-123	7	9
β-strand	126-128	3	9
β-strand	132-134	3	8
β-strand	138-139	2	8
β-strand	145-153	9	8
β-strand	161-167	7	9
β-strand	174-178	5	9

Chain G: 7 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	47-49	3	7
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
α-helix	90-92	3
β-strand	95	1	10
β-strand	98-103	6	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
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 H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1-9	9

2 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	205	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	246	Homo sapiens
DQ2-glia-omega1 peptide	C, H	protein	13	Homo sapiens

Sequence of entity 1 (A, F), FASTA

>7SG2_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A, F)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPE

Sequence of entity 2 (B, G), FASTA

>7SG2_2 MHC class II HLA-DQ-beta-1 (chains B, G)
GGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEF
RAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTE
ALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQR
GDVYTCHVEHPSLQSPITVEWRAQS

Sequence of entity 3 (D, I), FASTA

>7SG2_3 T-cell receptor, xpa5, alpha chain (chains D, I)
HMKTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEVA
SLFIPADRKSSTLSLPRVSLSDTAVYYCLVGGLARDMRFGAGTRLTVKPNIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E, J), FASTA

>7SG2_4 T-cell receptor, xpa5, beta chain (chains E, J)
HMAVISQKPSRDICQRGTSLTIQCQVDSQVTMMFWYRQQPGQSLTLIATANQGSEATYES
GFVIDKFPISRPNLTFSTLTVSNMSPEDSSIYLCSVALGSDTGELFFGEGSRLTVLEDLK
NVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Sequence of entity 5 (C, H), FASTA

>7SG2_5 DQ2-glia-omega1 peptide (chains C, H)
QPFPQPEQPFPGS

Ligands and cofactors

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

Water and common crystallization additives (ACT, 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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