9EJH: PDB entry 9EJH

Peptide-independent T cell receptor recognition of HLA-DQ2. Determined by X-ray diffraction at 2.45 Å resolution. Released 26 Mar 2025.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,638
Mol. weight: 95.53 kDa
Ligands: NAG
Released: 26 Mar 2025

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

Secondary structure: helices and β-sheets

9EJH contains 29 α-helices and 71 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: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	7-16	11	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	42-45	4	1
α-helix	48-52	5
α-helix	58-78	21
α-helix	83-87	5
β-strand	90-95	6	2
β-strand	105-114	10	2
β-strand	120-125	6	3
β-strand	128-130	3	3
β-strand	134-136	3	2
α-helix	139	1
β-strand	140-141	2	2
β-strand	147-155	9	2
β-strand	163-168	6	3
β-strand	176-180	5	3

Chain B: 9 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	55-62	8
α-helix	65-74	10
α-helix	75-79	5
α-helix	80-88	9
α-helix	90-92	3
β-strand	95	1	4
α-helix	96-97	2
β-strand	98-104	7	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
α-helix	165-166	2
β-strand	170-176	7	6
β-strand	184-189	6	6

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3

Chain D: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
α-helix	10	1
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	132-137	6	9
β-strand	138	1	10
β-strand	145-150	6	9
α-helix	159-161	3
β-strand	166-168	3	9
β-strand	172-176	5	9
α-helix	177-179	3
β-strand	181-190	10	9
α-helix	197-200	4
β-strand	211	1	9

Chain E: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-24	6	11
α-helix	25	1
β-strand	38-45	8	12
β-strand	49-57	9	12
β-strand	64-68	5	12
β-strand	76-80	5	11
β-strand	87-91	5	11
α-helix	96-98	3
β-strand	100-107	8	12
β-strand	116-117	2	12
β-strand	121-126	6	12
α-helix	129-131	3
β-strand	133	1	13
α-helix	134-135	2
β-strand	136-140	5	10
α-helix	141-143	3
α-helix	144-150	7
β-strand	152-162	11	10
β-strand	163	1	13
β-strand	167-173	7	14
β-strand	176-178	3	14
β-strand	182-184	3	10
α-helix	188	1
β-strand	189-190	2	10
β-strand	200-209	10	10
α-helix	210-213	4
β-strand	220-226	7	14
β-strand	229	1	15
α-helix	240-241	2
β-strand	243	1	15
β-strand	245-251	7	14

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	194	Homo sapiens	O19712 (AlphaFold model)
HLA class II histocompatibility antigen gamma chain	C	protein	13	Homo sapiens	P04233 (AlphaFold model)
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

>9EJH_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWSLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPE

Sequence of entity 2 (B), FASTA

>9EJH_2 MHC class II HLA-DQ-beta-1 (chains B)
RDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEY
WNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVT
DFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSL
QSPITVEWRAQSTG

Sequence of entity 3 (C), FASTA

>9EJH_3 HLA class II histocompatibility antigen gamma chain (chains C)
ATPLLMQALPMGA

Sequence of entity 4 (D), FASTA

>9EJH_4 G9 T cell receptor alpha chain (chains D)
MQRKEVEQDPGPFNVPEGATVAFNCTYSNSASQSFFWYRQDCRKEPKLLMSVYSSGNEDG
RFTAQLNRASQYISLLIRDSKLSDSATYLCVVMGFQKLVFGTGTRLLVSPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>9EJH_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	2

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 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
6MFF 2.6 Å, HLA-DQ2-glia-omega1

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