8ZJY: PAg-bound BTN2A1-BTN3A1-BTN3A3

Cryo-EM structure of pAg-bound BTN2A1-BTN3A1-BTN3A3 in complex with Vgamma9-Vdelta2 TCR (G115 genotype). Determined by electron microscopy at 3.7 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Homo sapiens
Chains: 6
Atoms: 18,974
Mol. weight: 290.46 kDa
Ligands: H6P
Released: 26 Nov 2025

Explore 8ZJY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZJY contains 35 α-helices and 201 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: 7 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	1
β-strand	40-42	3	2
β-strand	48-49	2	3
β-strand	52	1	1
α-helix	59-61	3
β-strand	63-67	5	4
β-strand	74	1	5
β-strand	76-79	4	4
β-strand	82-83	2	4
β-strand	88	1	5
β-strand	97-99	3	3
β-strand	107	1	1
β-strand	109-111	3	3
β-strand	122-129	8	4
β-strand	132-139	8	4
β-strand	141-143	3	2
β-strand	144	1	6
α-helix	148-149	2
β-strand	150-153	4	7
β-strand	161-167	7	7
β-strand	171	1	6
β-strand	175-179	5	8
β-strand	186	1	8
β-strand	190-194	5	7
β-strand	202-209	8	7
β-strand	216-222	7	8
β-strand	229-235	7	8
α-helix	250-320	71
β-strand	325-327	3	9
β-strand	332	1	10
α-helix	334-336	3
β-strand	341-343	3	9
β-strand	349-352	4	9
α-helix	353-355	3
β-strand	374-376	3	11
β-strand	377	1	10
β-strand	381	1	11
β-strand	385-391	7	9
β-strand	398-404	7	11
β-strand	421-427	7	11
β-strand	430-432	3	11
β-strand	440	1	11
β-strand	449-455	7	9
β-strand	460-465	6	9
β-strand	470-474	5	9
α-helix	475-477	3
β-strand	484-490	7	11
β-strand	497-499	3	9
α-helix	500-503	4
β-strand	516-517	2	9

Chain B: 7 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	12
α-helix	38	1
β-strand	39-42	4	13
β-strand	47-51	5	14
β-strand	52-54	3	12
β-strand	63-67	5	13
β-strand	74	1	15
β-strand	76-79	4	13
β-strand	82-84	3	13
β-strand	88	1	15
α-helix	90-92	3
β-strand	96-99	4	14
β-strand	108-112	5	14
β-strand	121-129	9	13
β-strand	132-143	12	13
β-strand	144	1	16
α-helix	147-149	3
β-strand	150-157	8	17
β-strand	160-170	11	17
β-strand	171	1	16
β-strand	175-179	5	18
β-strand	190-195	6	17
β-strand	201-209	9	17
β-strand	216	1	19
β-strand	218-223	6	18
β-strand	228-232	5	18
β-strand	235	1	19
α-helix	247-321	75
β-strand	325-327	3	9
β-strand	332	1	20
α-helix	334-336	3
β-strand	342-343	2	9
β-strand	349-351	3	9
β-strand	374-376	3	21
β-strand	377	1	20
β-strand	381	1	21
β-strand	385-391	7	9
β-strand	398-404	7	21
β-strand	421-427	7	21
β-strand	430-432	3	21
β-strand	440	1	21
β-strand	449-455	7	9
β-strand	460-465	6	9
β-strand	470-474	5	9
α-helix	475-477	3
β-strand	484-490	7	21
β-strand	497-499	3	9
α-helix	500-503	4
β-strand	516-517	2	9

Chain D: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	22
β-strand	19-22	4	23
α-helix	30-32	3
β-strand	33-40	8	22
β-strand	46-51	6	22
β-strand	55-56	2	22
β-strand	64-69	6	23
β-strand	74-79	6	23
β-strand	88-96	9	22
α-helix	97	1
β-strand	108-116	9	22
β-strand	125	1	24
β-strand	128-134	7	25
β-strand	137-145	9	25
β-strand	146	1	24
β-strand	151-154	4	26
β-strand	161-162	2	25
β-strand	166-169	4	25
β-strand	175-182	8	25
β-strand	191-195	5	26
β-strand	198-201	4	26

Chain E: 7 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	27
β-strand	40-43	4	28
β-strand	48-53	6	27
β-strand	64-69	6	28
β-strand	75-79	5	28
β-strand	80	1	29
β-strand	83	1	29
β-strand	97-100	4	27
β-strand	108-113	6	27
β-strand	122-130	9	28
β-strand	133-144	12	28
β-strand	145	1	30
β-strand	151-158	8	31
β-strand	161-171	11	31
β-strand	172	1	30
β-strand	176-180	5	32
α-helix	185	1
β-strand	186-187	2	32
α-helix	188	1
β-strand	190-191	2	31
α-helix	192-194	3
β-strand	202-210	9	31
β-strand	217-224	8	32
β-strand	229-237	9	32
α-helix	239-241	3
α-helix	246-319	74
α-helix	325-331	7
β-strand	338	1	33
β-strand	343-344	2	34
β-strand	354-355	2	35
β-strand	361-363	3	35
β-strand	386-387	2	34
β-strand	394-399	6	33
β-strand	408-412	5	36
α-helix	427-429	3
β-strand	431-437	7	36
β-strand	441-444	4	36
β-strand	450-452	3	36
β-strand	461-466	6	33
β-strand	472-476	5	33
β-strand	482-486	5	33
β-strand	496-500	5	36
β-strand	509-510	2	35

Chain F: 9 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	32-34	3	37
β-strand	42-43	2	38
β-strand	48-51	4	39
β-strand	53-55	3	37
β-strand	64-69	6	40
β-strand	75-79	5	40
β-strand	80	1	41
β-strand	83	1	41
α-helix	91-93	3
β-strand	97-100	4	39
α-helix	104-106	3
β-strand	110-113	4	39
β-strand	122-130	9	40
β-strand	133-141	9	40
β-strand	143-144	2	38
β-strand	145	1	42
α-helix	148-150	3
β-strand	151-158	8	32
β-strand	161-171	11	32
β-strand	172	1	42
β-strand	178-181	4	31
β-strand	186	1	31
β-strand	190	1	32
β-strand	202-210	9	32
β-strand	216-224	9	31
β-strand	229-237	9	31
α-helix	239-242	4
α-helix	247-320	74
α-helix	321-323	3
α-helix	326-336	11
β-strand	338-339	2	43
β-strand	344	1	44
α-helix	346-348	3
β-strand	353-355	3	45
β-strand	362-364	3	45
β-strand	383-385	3	46
β-strand	386	1	44
β-strand	390	1	47
β-strand	394-400	7	43
β-strand	407-412	6	46
α-helix	426-428	3
β-strand	430-436	7	46
β-strand	440-443	4	46
β-strand	449-451	3	46
β-strand	460-465	6	43
β-strand	470-475	6	43
β-strand	481-486	6	43
β-strand	494	1	47
β-strand	495-499	5	46
β-strand	509-510	2	43

Chain G: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	48
β-strand	10-14	5	49
β-strand	18-26	9	48
β-strand	35-40	6	49
β-strand	47-52	6	49
β-strand	58-60	3	49
β-strand	69-74	6	48
β-strand	79-85	7	48
β-strand	93-102	10	49
α-helix	103	1
β-strand	109-113	5	49
β-strand	117-122	6	49
β-strand	133-137	5	50
β-strand	143	1	51
β-strand	146	1	51
β-strand	152-159	8	50
β-strand	165-170	6	52
β-strand	180-181	2	50
β-strand	191-197	7	50
β-strand	208-213	6	52
α-helix	218-220	3
α-helix	221-222	2
β-strand	223-227	5	52

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Butyrophilin subfamily 2 member A1	A, B	protein	534	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 A3	E	protein	589	Homo sapiens	O00478 (AlphaFold model)
Butyrophilin subfamily 3 member A1	F	protein	484	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

>8ZJY_1 Butyrophilin subfamily 2 member A1 (chains A, B)
MDMRVPAQLLGLLLLWLSGARCQFIVVGPTDPILATVGENTTLRCHLSPEKNAEDMEVRW
FRSQFSPAVFVYKGGRERTEEQMEEYRGRTTFVSKDISRGSVALVIHNITAQENGTYRCY
FQEGRSYDEAILHLVVAGLGSKPLISMRGHEDGGIRLECISRGWYPKPLTVWRDPYGGVA
PALKEVSMPDADGLFMVTTAVIIRDKSVRNMSCSINNTLLGQKKESVIFIPESFMPSVSP
CAVALPIIVVILMIPIAVCIYWINKLQKEKKILSGEKEFERETREIALKELEKERVQKEE
ELQVKEKLQEELRWRRTFLHAVDVVLDPDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNP
ERFDSQPCVLGRESFASGKHYWEVEVENVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEM
HKGQYRAVSSPDRILPLKESLCRVGVFLDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRP
FFRLGCEDSPIFICPALTGANGVTVPEEGLTLHRVGTHQSLGSSGMDYKDDDDK

Sequence of entity 2 (D), FASTA

>8ZJY_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

>8ZJY_3 Butyrophilin subfamily 3 member A3 (chains E)
MDMRVPAQLLGLLLLWLSGARCQFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELRW
VSSSLRQVVNVYADGKEVEDRQSAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCY
FQDGDFYEKALVELKVAALGSDLHIEVKGYEDGGIHLECRSTGWYPQPQIKWSDTKGENI
PAVEAPVVADGVGLYAVAASVIMRGSSGGGVSCIIRNSLLGLEKTASISIADPFFRSAQP
WIAALAGTLPISLLLLAGASYFLWRQQKEKIALSRETEREREMKEMGYAATEQEISLREK
LQEELKWRKIQYMARGEKSLAYHEWKMALFKPADVILDPDTANAILLVSEDQRSVQRAEE
PRDLPDNPERFEWRYCVLGCENFTSGRHYWEVEVGDRKEWHIGVCSKNVERKKGWVKMTP
ENGYWTMGLTDGNKYRALTEPRTNLKLPEPPRKVGIFLDYETGEISFYNATDGSHIYTFP
HASFSEPLYPVFRILTLEPTALTICPIPKEVESSPDPDLVPDHSLETPLTPGLANESGEP
QAEVTSLLLPAHPGAEVSPSATTNQNHKLQARTEALYGSSGHHHHHHHH

Sequence of entity 4 (F), FASTA

>8ZJY_4 Butyrophilin subfamily 3 member A1 (chains F)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSD
LHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVI
MRGSSGEGVSCTIRSSLLGLEKTASISIADPFFRSAQRWIAALAGTLPVLLLLLGGAGYF
LWQQQEEKKTQFRKKKREQELREMAWSTMKQEQSTRVKLLEELRWRSIQYASRGERHSAY
NEWKKALFKPADVILDPKTANPILLVSEDQRSVQRAKEPQDLPDNPERFNWHYCVLGCES
FISGRHYWEVEVGDRKEWHIGVCSKNVQRKGWVKMTPENGFWTMGLTDGNKYRTLTEPRT
NLKLPKPPKKVGVFLDYETGDISFYNAVDGSHIHTFLDVSFSEALYPVFRILTLEPTALT
ICPA

Sequence of entity 5 (G), FASTA

>8ZJY_5 T cell receptor gamma variable 9, T cell receptor gamma constant 1 (chains G)
GHLEQPQISSTKTLSKTARLECVVSGITISATSVYWYRERPGEVIQFLVSISYDGTVRKE
SGIPSGKFEVDRIPETSTSTLTIHNVEKQDIATYYCALWEAQQELGKKIKVFGPGTKLII
TDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILGSQE
GNTMKTNDTYMKFSWLTVPEESLDKEHRCIVRHENNKNGVDQEIIFPPI

Ligands and cofactors

ID	Name	Formula	Copies
H6P	(2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate	C5 H12 O8 P2	1

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
9IRD 3.2 Å, Cryo-EM structure of BTN2A1-BTN3A1-BTN3A2 mutant (BTN3A1 H381R, BTN2A1 R477A/T510A) in…
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…

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