9EJI: PDB entry 9EJI

Peptide-independent T cell receptor recognition of HLA-DQ2. Determined by X-ray diffraction at 2.2 Å resolution. Released 26 Mar 2025.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 5
Atoms: 7,042
Mol. weight: 96.36 kDa
Ligands: NAG
Released: 26 Mar 2025

Explore 9EJI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EJI contains 28 α-helices and 70 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	4-14	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	55-75	21
α-helix	80-84	5
β-strand	87-92	6	2
β-strand	102-111	10	2
β-strand	117-122	6	3
β-strand	125-127	3	3
β-strand	131-133	3	2
α-helix	136	1
β-strand	137-138	2	2
β-strand	144-152	9	2
β-strand	160-165	6	3
β-strand	173-177	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	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-87	7
α-helix	90-92	3
β-strand	95	1	4
α-helix	96-97	2
β-strand	98-103	6	5
β-strand	114-122	9	5
β-strand	123	1	4
β-strand	128-133	6	6
β-strand	136-138	3	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	184-188	5	6

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
α-helix	5-11	7

Chain D: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
β-strand	11-14	4	8
β-strand	19-25	7	7
β-strand	38-44	7	8
β-strand	50-55	6	8
β-strand	57	1	7
β-strand	65-68	3	7
β-strand	76-81	6	7
β-strand	86-91	6	7
α-helix	96-98	3
β-strand	100-108	9	8
β-strand	111-114	4	8
β-strand	118-123	6	8
α-helix	124	1
β-strand	132-135	4	9
α-helix	136-139	4
β-strand	145-150	6	9
α-helix	159-161	3
β-strand	167-168	2	9
α-helix	169-171	3
β-strand	172-176	5	9
β-strand	181-190	10	9
α-helix	197-199	3
β-strand	211	1	9

Chain E: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	10
β-strand	10-14	5	8
β-strand	19-24	6	10
α-helix	25-26	2
β-strand	38-44	7	8
β-strand	51-57	7	8
β-strand	64-68	5	8
β-strand	76-80	5	10
β-strand	87-91	5	10
α-helix	96-98	3
β-strand	100-107	8	8
β-strand	116-117	2	8
β-strand	121-126	6	8
α-helix	129-131	3
β-strand	133	1	11
α-helix	134-135	2
β-strand	136-140	5	12
α-helix	141-143	3
α-helix	144-150	7
β-strand	152-162	11	12
β-strand	163	1	11
β-strand	167-173	7	13
β-strand	176-178	3	13
β-strand	182-184	3	12
α-helix	188	1
β-strand	189-190	2	12
β-strand	200-209	10	12
α-helix	210-214	5
β-strand	219-226	8	13
β-strand	229	1	14
α-helix	240-241	2
β-strand	243	1	14
β-strand	245-252	8	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen DQ alpha chain	A	protein	184	Homo sapiens	Q08AS3 (AlphaFold model)
HLA class II histocompatibility antigen DQ beta chain	B	protein	196	Homo sapiens	A0A0U5IHY9 (AlphaFold model)
glut-L1 peptide	C	protein	13	Triticum aestivum
G9 T cell receptor alpha chain	D	protein	204	Homo sapiens
G9 T cell receptor beta chain	E	protein	242	Homo sapiens

Sequence of entity 1 (A), FASTA

>9EJI_1 HLA class II histocompatibility antigen DQ alpha chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQFTHEFDGDEEFYVDLERKETVWKLPLFHRLRFDPQF
ALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHW
EPET

Sequence of entity 2 (B), FASTA

>9EJI_2 HLA class II histocompatibility antigen DQ beta chain (chains B)
RDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEY
WNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVT
DFYPAQIKVRWFRNGQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSL
QSPITVEWRAQSESAQ

Sequence of entity 3 (C), FASTA

>9EJI_3 glut-L1 peptide (chains C)
QPPASEQEQPVLP

Sequence of entity 4 (D), FASTA

>9EJI_4 G9 T cell receptor alpha chain (chains D)
MQRKEVEQDPGPFNVPEGATVAFNCTYSNSASQSFFWYRQDCRKEPKLLMSVYSSGNEDG
RFTAQLNRASQYISLLIRDSKLSDSATYLCVVMGFQKLVFGTGTRLLVSPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>9EJI_5 G9 T cell receptor beta chain (chains E)
MGVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFP
GRFSGRQFSNSRSEMNVSTLELGDSALYLCASSLRAESGELFFGEGSRLTVLEDLNKVFP
PEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (GOL, ACT) are not listed.

Primary citation

A naturally selected alpha beta T cell receptor binds HLA-DQ2 molecules without co-contacting the presented peptide. Lim, J.J., Jones, C.M., Loh, T.J. et al. Nat Commun (2025) 16:3330-3330. DOI 10.1038/s41467-025-58690-w · PubMed

Other PDB entries of the same protein (UniProt Q08AS3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RUG 2.74 Å, Cryo-EM structure of the LB_DQB0303_A Fab - HLA-DQB1*03:03/DQA1*02:01 human…
6PY2 2.83 Å, HLA-TCR complex
6PX6 3.0 Å, HLA-TCR complex

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