9O4X: Gamma delta T cell receptor

Gamma delta T cell receptor bound to CD1d. Determined by X-ray diffraction at 2.86 Å resolution. Released 10 Dec 2025.

Method: X-ray diffraction
Resolution: 2.86 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,542
Mol. weight: 92.98 kDa
Ligands: NAG, FO4
Released: 10 Dec 2025

Explore 9O4X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9O4X contains 27 α-helices and 68 β-strands across 4 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-19	10	12
β-strand	23-32	10	12
β-strand	35-40	6	12
α-helix	47	1
β-strand	48-49	2	12
α-helix	60-87	28
α-helix	90-91	2
α-helix	93	1
β-strand	94-105	12	12
β-strand	109-118	10	12
β-strand	121-127	7	12
β-strand	130-133	4	12
α-helix	134	1
α-helix	139-150	12
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	13
β-strand	188-193	6	14
β-strand	201-211	11	14
β-strand	212	1	13
β-strand	217-222	6	15
β-strand	225-226	2	15
β-strand	231-232	2	14
β-strand	236-237	2	14
α-helix	238	1
β-strand	243-252	10	14
β-strand	260-264	5	15
α-helix	266-268	3
β-strand	273-276	4	15

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	6-11	6	1
β-strand	21-30	10	1
β-strand	35-41	7	2
β-strand	44-45	2	2
β-strand	50-51	2	1
α-helix	52-54	3
β-strand	55-56	2	1
β-strand	62-70	9	1
β-strand	78-84	7	2
β-strand	91-94	4	2
α-helix	95-96	2

Chain D: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	3
β-strand	13-17	5	4
β-strand	21-24	4	3
β-strand	27-29	3	3
β-strand	36-42	7	4
β-strand	48-55	8	4
β-strand	62-63	2	3
β-strand	66-71	6	3
β-strand	76-82	7	3
α-helix	86-88	3
β-strand	90-97	8	4
β-strand	104-105	2	4
β-strand	109-114	6	4
α-helix	115-117	3
β-strand	121	1	5
β-strand	125-130	6	6
β-strand	133-141	9	6
β-strand	142	1	5
β-strand	147-150	4	7
β-strand	155-158	4	6
α-helix	160-161	2
β-strand	162-165	4	6
β-strand	171-179	9	6
α-helix	182-184	3
β-strand	187-191	5	7
β-strand	194-197	4	7
α-helix	198-200	3

Chain G: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	8
β-strand	22-25	4	9
β-strand	35-41	7	8
β-strand	48-54	7	8
β-strand	59-62	4	8
α-helix	63	1
α-helix	66-67	2
β-strand	71-74	4	9
β-strand	82-85	4	9
α-helix	90-92	3
β-strand	94-101	8	8
β-strand	108-110	3	8
β-strand	114-118	5	8
α-helix	129	1
β-strand	130-134	5	10
α-helix	135-137	3
α-helix	138-144	7
β-strand	146-156	11	10
β-strand	161-167	7	11
β-strand	177-178	2	10
β-strand	182-184	3	10
β-strand	187-197	11	10
β-strand	205-211	7	11
α-helix	215-217	3
β-strand	220-224	5	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
T cell receptor delta chain	D	protein	197	Homo sapiens
T cell receptor gamma chain	G	protein	224	Homo sapiens
Antigen-presenting glycoprotein CD1d	A	protein	274	Homo sapiens	P15813 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9O4X_1 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 2 (D), FASTA

>9O4X_2 T cell receptor delta chain (chains D)
QKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKSG
RYSVNFKKAAKSVALTISALQLEDSAKYFCALGVWGDKLIFGKGTRVTVEPRSQPHTKPS
VFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLGKYEDSNS
VTCSVQHDNKTVHSTDF

Sequence of entity 3 (G), FASTA

>9O4X_3 T cell receptor gamma chain (chains G)
SSNLEGGTKSVTRPTRSSAEITCDLTVINAFYIHWYLHQEGKAPQRLLYYDVSNSKDVLE
SGLSPGKYYTHTPRRWSWILILRNLIENDSGVYYCATWDRLYYKKLFGSGTTLVVTDKQL
DADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILGSQEGNTMK
TNDTYMKFSWLTVPEESLDKEHRCIVRHENNKNGVDQEIIFPPI

Sequence of entity 4 (A), FASTA

>9O4X_4 Antigen-presenting glycoprotein CD1d (chains A)
RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWET
LQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILS
FQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQV
KPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYL
RATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWGS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
FO4	sphingomyelin	C47 H94 N2 O6 P	1

Water and common crystallization additives (1PE) are not listed.

Primary citation

gamma delta T cell receptor recognition of CD1d in a lipid-independent manner. Rice, M.T., Gunasinghe, S.D., Sok, C.L. et al. Nat Commun (2025) 17:926-926. DOI 10.1038/s41467-025-67653-0 · PubMed

Other PDB entries of the same protein (UniProt P61769 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4E0K 0.97 Å, Crystal Structure of the amyloid-fibril forming peptide KDWSFY derived from human Beta 2…
1K5N 1.09 Å, HLA-B*2709 bound to nona-peptide M9
3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
2YXF 1.13 Å, The high resolution crystal structure of beta2-microglobulin under physiological…
8E2Z 1.13 Å, Structures of HLA-B8E76C loaded with long peptides reveal novel features at the…
7NMR 1.15 Å, Crystal structure of beta-2-microglobulin D76S mutant
8ROP 1.15 Å, Crystal structure of HLA B*18:01 in complex with QEIRTFSF, an 8-mer epitope from…
7R7W 1.17 Å, Crystal structure of HLA-B*5301 complex with an HIV-1 Gag-derived epitope QW9 S3T variant
4U1M 1.18 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
6Y26 1.2 Å, Crystal structure of HLA-B2705 complexed with the nona-peptide mA
7NMC 1.2 Å, Crystal structure of beta-2-microglobulin D76E mutant

Browse structure collections

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