9IRD: BTN2A1-BTN3A1-BTN3A2 mutant

Cryo-EM structure of BTN2A1-BTN3A1-BTN3A2 mutant (BTN3A1 H381R, BTN2A1 R477A/T510A) in complex with Vgamma9-Vdelta2 TCR (G115 genotype). Determined by electron microscopy at 3.2 Å resolution. Released 18 Feb 2026.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,010
Mol. weight: 142.62 kDa
Released: 18 Feb 2026

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

Secondary structure: helices and β-sheets

9IRD contains 22 α-helices and 130 β-strands across 6 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: 1 helix, 22 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	1
β-strand	39-41	3	2
β-strand	47-51	5	3
β-strand	52-54	3	1
β-strand	64-67	4	2
β-strand	74	1	4
β-strand	76-79	4	2
β-strand	82-83	2	2
β-strand	88	1	4
β-strand	96-99	4	3
β-strand	108-112	5	3
β-strand	121-129	9	2
β-strand	132-142	11	2
β-strand	150-152	3	5
β-strand	156-157	2	5
β-strand	160-170	11	5
β-strand	175-179	5	6
β-strand	185-186	2	6
β-strand	190-195	6	5
α-helix	196	1
β-strand	201-209	9	5
β-strand	216-222	7	6
β-strand	229-235	7	6

Chain B: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	7
α-helix	38	1
β-strand	39-42	4	8
β-strand	47-54	8	7
β-strand	63-67	5	8
β-strand	74	1	9
β-strand	76-79	4	8
β-strand	82-83	2	8
β-strand	88	1	9
β-strand	96-99	4	7
α-helix	103-105	3
β-strand	107-112	6	7
β-strand	121-129	9	8
β-strand	132-143	12	8
β-strand	144	1	10
α-helix	147-149	3
β-strand	150	1	11
β-strand	153-156	4	12
β-strand	161-163	3	12
β-strand	165-170	6	11
β-strand	171	1	10
β-strand	175-179	5	13
α-helix	186-188	3
β-strand	190-195	6	11
β-strand	201-206	6	11
β-strand	208-209	2	12
β-strand	216-223	8	13
β-strand	228-235	8	13

Chain D: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	14
β-strand	10-13	4	15
β-strand	19-24	6	14
α-helix	30-32	3
β-strand	33-40	8	16
β-strand	46-51	6	16
β-strand	55-56	2	16
β-strand	64-69	6	14
β-strand	74-79	6	14
β-strand	88	1	15
β-strand	89-96	8	16
β-strand	107-109	3	16
β-strand	114-117	4	15
α-helix	118-121	4
β-strand	125	1	17
β-strand	128-134	7	18
β-strand	137-145	9	18
β-strand	146	1	17
β-strand	150-155	6	19
β-strand	159-162	4	18
β-strand	166-169	4	18
β-strand	175-183	9	18
β-strand	190-195	6	19
β-strand	198-201	4	19

Chain E: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	32-34	3	20
β-strand	40-43	4	21
β-strand	48-55	8	20
β-strand	64-69	6	21
β-strand	74-80	7	21
β-strand	83-84	2	21
α-helix	91-93	3
β-strand	97-100	4	20
α-helix	104-106	3
β-strand	108-113	6	20
β-strand	122-130	9	21
β-strand	133-144	12	21
β-strand	145	1	22
α-helix	147-150	4
β-strand	151-158	8	23
β-strand	161-171	11	23
β-strand	172	1	22
β-strand	176-181	6	24
β-strand	186-187	2	24
β-strand	190-191	2	23
α-helix	192-194	3
β-strand	195	1	23
β-strand	202-210	9	23
β-strand	217-223	7	24
β-strand	230-237	8	24
α-helix	239-241	3

Chain F: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	32-34	3	25
β-strand	39-42	4	26
β-strand	48-52	5	27
β-strand	53-55	3	25
β-strand	64-69	6	26
β-strand	74-80	7	26
β-strand	83-85	3	26
α-helix	91-93	3
β-strand	98-100	3	27
β-strand	109-113	5	27
α-helix	118-120	3
β-strand	122-129	8	26
β-strand	136-143	8	26
β-strand	145	1	28
β-strand	151-158	8	24
β-strand	161-171	11	24
β-strand	172	1	28
α-helix	175	1
β-strand	176-180	5	23
β-strand	186-187	2	23
α-helix	188	1
β-strand	202-210	9	24
β-strand	218-224	7	23
α-helix	225-227	3
β-strand	229-237	9	23
α-helix	239-241	3

Chain G: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	29
β-strand	10-13	4	30
β-strand	19-26	8	29
β-strand	35-40	6	30
β-strand	46-52	7	30
β-strand	58-60	3	30
α-helix	65	1
β-strand	69-74	6	29
β-strand	79-84	6	29
α-helix	89-91	3
β-strand	93-102	10	30
β-strand	109-113	5	30
β-strand	117-121	5	30
α-helix	125-126	2
β-strand	133-137	5	31
β-strand	143	1	32
β-strand	146	1	32
β-strand	150-157	8	31
β-strand	165-169	5	33
β-strand	180-181	2	31
β-strand	185	1	31
β-strand	192-199	8	31
β-strand	208-213	6	33
α-helix	218-220	3
β-strand	223-227	5	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Butyrophilin subfamily 2 member A1	A, B	protein	214	Homo sapiens	Q7KYR7 (AlphaFold model)
T cell receptor delta variable 2,T cell receptor delta constant 1	D	protein	204	Homo sapiens
Butyrophilin subfamily 3 member A2	E	protein	213	Homo sapiens	P78410 (AlphaFold model)
Butyrophilin subfamily 3 member A1	F	protein	214	Homo sapiens	O00481 (AlphaFold model)
T cell receptor gamma variable 9,T cell receptor gamma constant 1	G	protein	229	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>9IRD_1 Butyrophilin subfamily 2 member A1 (chains A, B)
QFIVVGPTDPILATVGENTTLRCHLSPEKNAEDMEVRWFRSQFSPAVFVYKGGRERTEEQ
MEEYRGRTTFVSKDISRGSVALVIHNITAQENGTYRCYFQEGRSYDEAILHLVVAGLGSK
PLISMRGHEDGGIRLECISRGWYPKPLTVWRDPYGGVAPALKEVSMPDADGLFMVTTAVI
IRDKSVRNMSCSINNTLLGQKKESVIFIPESFMP

Sequence of entity 2 (D), FASTA

>9IRD_2 T cell receptor delta variable 2,T cell receptor delta constant 1 (chains D)
IELVPEHQTVPVSIGVPATLRCSMKGEAIGNYYINWYRKTQGNTMTFIYREKDIYGPGFK
DNFQGDIDIAKNLAVLKILAPSERDEGSYYCASDTLGMGGEYTDKLIFGKGTRVTVEPRS
QPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLG
KYEDSNSVTCSVQHDNKTVHSTDF

Sequence of entity 3 (E), FASTA

>9IRD_3 Butyrophilin subfamily 3 member A2 (chains E)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSN
LHVEVKGYEDGGIHLECRSTGWYPQPQIQWSNAKGENIPAVEAPVVADGVGLYEVAASVI
MRGGSGEGVSCIIRNSLLGLEKTASISIADPFF

Sequence of entity 4 (F), FASTA

>9IRD_4 Butyrophilin subfamily 3 member A1 (chains F)
AQFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDR
QSAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGS
DLHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASV
IMRGSSGEGVSCTIRSSLLGLEKTASISIADPFF

Sequence of entity 5 (G), FASTA

>9IRD_5 T cell receptor gamma variable 9,T cell receptor gamma constant 1 (chains G)
GHLEQPQISSTKTLSKTARLECVVSGITISATSVYWYRERPGEVIQFLVSISYDGTVRKE
SGIPSGKFEVDRIPETSTSTLTIHNVEKQDIATYYCALWEAQQELGKKIKVFGPGTKLII
TDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILGSQE
GNTMKTNDTYMKFSWLTVPEESLDKEHRCIVRHENNKNGVDQEIIFPPI

Primary citation

Phosphoantigen-driven dissociation of butyrophilin oligomers activates gamma delta T cells. Xin, W., Huang, B., Gao, W. et al. Cell Discov (2026) 12. DOI 10.1038/s41421-026-00911-7 · PubMed

Other PDB entries of the same protein (UniProt Q7KYR7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8IGT 1.56 Å, Crystal Structure of Intracellular B30.2 Domain of BTN2A1
8DFW 2.1 Å, Crystal Structure of Human BTN2A1 in Complex With Vgamma9-Vdelta2 T Cell Receptor
8JYE 2.18 Å, Crystal Structure of Intracellular B30.2 Domain of BTN3A1 and BTN2A1 in Complex with HMBPP
8JYC 2.29 Å, Crystal Structure of Intracellular B30.2 Domain of BTN3A1 and BTN2A1 in Complex with DMAPP
8VC7 2.76 Å, Crystal Structure of Human BTN2A1 ectodomain in complex with Antagonist 2A1.9 Fab
8ZHR 3.0 Å, Cryo-EM structure of the full-length pAg-bound BTN2A1-BTN3A1-BTN3A2 complex
9JQR 3.0 Å, Cryo-EM structure of the Vgamma9Vdelta2 TCR-engaged BTN3A1-BTN3A2-BTN2A1 complex
9JQQ 3.26 Å, Cryo-EM structure of the HMBPP-primed BTN3A1-BTN3A2-BTN2A1 complex
9II6 3.27 Å, Cryo-EM structure of the intracellular domains of BTN2A1-BTN3A1-BTN3A3
9JQ6 3.34 Å, Cryo-EM structure of BTN2A1 in complex with antagonist antibody TH002
9JQP 3.34 Å, Cryo-EM structure of the HMBPP-primed BTN3A1-BTN3A2-BTN2A1 in complex with agonist…
8ZJX 3.35 Å, Cryo-EM structure of the full length pAg-bound BTN2A1-BTN3A1-BTN3A2 in complex with…

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