9JQR: Butyrophilin subfamily 3 member A1

Cryo-EM structure of the Vgamma9Vdelta2 TCR-engaged BTN3A1-BTN3A2-BTN2A1 complex. Determined by electron microscopy at 3.0 Å resolution. Released 18 Jun 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 17,295
Mol. weight: 280.21 kDa
Ligands: NAG, H6P
Released: 18 Jun 2025

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

Secondary structure: helices and β-sheets

9JQR contains 45 α-helices and 180 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: 6 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
α-helix	10	1
β-strand	11-14	4	2
β-strand	19	1	3
β-strand	22-23	2	4
β-strand	24-26	3	1
β-strand	35-38	4	5
β-strand	48-51	4	5
β-strand	54-56	3	5
β-strand	68	1	3
β-strand	71	1	4
α-helix	75-77	3
β-strand	80-81	2	4
β-strand	84	1	3
β-strand	95-101	7	5
β-strand	104-110	7	5
β-strand	112-115	4	2
β-strand	122-129	8	6
β-strand	132-140	9	6
β-strand	147-151	5	7
β-strand	157	1	7
β-strand	161-162	2	6
β-strand	174-180	7	6
β-strand	189-195	7	7
β-strand	200-207	8	7
α-helix	220-290	71
α-helix	297-307	11
β-strand	309-310	2	8
β-strand	315-320	6	9
β-strand	324-326	3	10
β-strand	332-335	4	10
α-helix	339-341	3
β-strand	354-357	4	9
β-strand	361	1	9
β-strand	365-368	4	8
β-strand	378-384	7	9
β-strand	401-406	6	9
β-strand	413-414	2	9
β-strand	420-421	2	9
β-strand	432-436	5	8
β-strand	441-445	5	8
β-strand	452-455	4	8
β-strand	465-470	6	9
β-strand	479-480	2	10
α-helix	481-483	3

Chain B: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	11
α-helix	10	1
β-strand	11-14	4	12
β-strand	19-26	8	11
β-strand	35-40	6	12
β-strand	45-51	7	12
β-strand	54-55	2	12
α-helix	57-59	3
α-helix	62-64	3
β-strand	68-71	4	11
α-helix	75-77	3
β-strand	79-84	6	11
β-strand	93-101	9	12
β-strand	104-115	12	12
β-strand	116	1	13
β-strand	122-127	6	7
β-strand	133-142	10	7
β-strand	143	1	13
α-helix	145-146	2
β-strand	147-151	5	6
α-helix	156	1
β-strand	157-158	2	6
α-helix	159	1
β-strand	161-162	2	7
α-helix	163-165	3
β-strand	166-167	2	7
β-strand	173-181	9	7
β-strand	189-195	7	6
β-strand	200-208	9	6
α-helix	210-214	5
α-helix	218-293	76

Chain D: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	14
β-strand	10-13	4	15
β-strand	19-25	7	14
α-helix	30-32	3
β-strand	33-40	8	16
β-strand	47-51	5	16
β-strand	55-56	2	16
β-strand	64-69	6	14
β-strand	74-79	6	14
α-helix	84-86	3
β-strand	88	1	15
β-strand	89-96	8	16
β-strand	107-109	3	16
β-strand	110	1	14
β-strand	114-117	4	15
α-helix	118-121	4
β-strand	129-134	6	17
β-strand	137-145	9	17
β-strand	152-155	4	18
β-strand	159-162	4	17
β-strand	166-169	4	17
β-strand	175-183	9	17
α-helix	186-188	3
β-strand	190-195	6	18
β-strand	198-201	4	18
α-helix	202-204	3

Chain E: 8 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	19
α-helix	10	1
β-strand	11-14	4	20
β-strand	19-23	5	21
β-strand	24-25	2	19
β-strand	35-38	4	22
β-strand	39	1	20
β-strand	48-51	4	22
β-strand	54-55	2	22
α-helix	62-64	3
β-strand	68-71	4	21
β-strand	80-84	5	21
α-helix	89-91	3
β-strand	93-96	4	20
β-strand	99-100	2	22
β-strand	105-106	2	22
β-strand	109-115	7	20
β-strand	116	1	23
α-helix	119-121	3
β-strand	122-128	7	24
β-strand	133-142	10	24
β-strand	143	1	23
β-strand	147-150	4	25
β-strand	151	1	26
β-strand	157	1	26
β-strand	162-167	6	24
β-strand	173-181	9	24
β-strand	188-194	7	25
β-strand	201-207	7	25
α-helix	228-295	68
β-strand	297-298	2	27
β-strand	304-305	2	28
α-helix	306-308	3
β-strand	313-315	3	29
β-strand	322-324	3	29
β-strand	346-347	2	30
β-strand	348-349	2	28
β-strand	353	1	30
β-strand	357-363	7	31
β-strand	371-376	6	30
β-strand	393-399	7	30
β-strand	402-405	4	30
β-strand	413	1	30
β-strand	421-427	7	31
β-strand	432	1	31
β-strand	435-437	3	31
β-strand	442-445	4	31
α-helix	447-449	3
β-strand	456-461	6	30
β-strand	470	1	31
α-helix	472-474	3
β-strand	489	1	32

Chain F: 10 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	33
β-strand	11-14	4	34
β-strand	19-23	5	35
β-strand	24-25	2	33
β-strand	35-39	5	34
β-strand	50	1	36
β-strand	55	1	36
α-helix	57-59	3
α-helix	62-64	3
β-strand	68-70	3	35
β-strand	80-84	5	35
α-helix	89-91	3
β-strand	93-101	9	34
β-strand	104-115	12	34
α-helix	119-121	3
β-strand	122-127	6	37
β-strand	134-142	9	37
β-strand	147-149	3	38
β-strand	162-164	3	37
β-strand	173-179	7	37
β-strand	191-194	4	38
β-strand	201-204	4	38
α-helix	228-294	67
β-strand	298-299	2	27
β-strand	304	1	39
α-helix	306-308	3
β-strand	349	1	39
β-strand	357-358	2	40
β-strand	361-363	3	32
β-strand	369-376	8	41
α-helix	384-386	3
β-strand	393-399	7	41
β-strand	402-405	4	41
β-strand	408	1	41
β-strand	421-423	3	32
β-strand	426-427	2	40
β-strand	432	1	40
β-strand	435-437	3	32
β-strand	442-445	4	32
α-helix	447-449	3
β-strand	456-462	7	41
α-helix	468-469	2
β-strand	470	1	32
α-helix	472-474	3

Chain G: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	42
β-strand	10-14	5	43
β-strand	18-26	9	42
β-strand	35-40	6	43
β-strand	47-52	6	43
β-strand	58-60	3	43
α-helix	65	1
β-strand	69-74	6	42
β-strand	79-85	7	42
α-helix	89-91	3
β-strand	93-102	10	43
β-strand	109-113	5	43
β-strand	117-122	6	43
β-strand	133-136	4	44
α-helix	141-142	2
α-helix	143-147	5
β-strand	149-153	5	45
β-strand	154-159	6	44
β-strand	164-170	7	46
β-strand	180-181	2	45
β-strand	185-187	3	44
β-strand	190-193	4	44
β-strand	195-200	6	45
β-strand	208-214	7	46
α-helix	218-220	3
α-helix	221-222	2
β-strand	223-227	5	46

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Butyrophilin subfamily 3 member A1	A	protein	527	Homo sapiens	O00481 (AlphaFold model)
Butyrophilin subfamily 3 member A2	B	protein	318	Homo sapiens	P78410 (AlphaFold model)
Vdelta2 T cell receptor	D	protein	274	Homo sapiens
Butyrophilin subfamily 2 member A1	E, F	protein	532	Homo sapiens	Q7KYR7 (AlphaFold model)
Vgamma9 T cell receptor	G	protein	295	Homo sapiens

Sequence of entity 1 (A), FASTA

>9JQR_1 Butyrophilin subfamily 3 member A1 (chains A)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSD
LHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVI
MRGSSGEGVSCTIRSSLLGLEKTASISIADPFFRSAQRWIAALAGTLPVLLLLLGGAGYF
LWQQQEEKKTQFRKKKREQELREMAWSTMKQEQSTRVKLLEELRWRSIQYASRGERHSAY
NEWKKALFKPADVILDPKTANPILLVSEDQRSVQRAKEPQDLPDNPERFNWHYCVLGCES
FISGRHYWEVEVGDRKEWHIGVCSKNVQRKGWVKMTPENGFWTMGLTDGNKYRTLTEPRT
NLKLPKPPKKVGVFLDYETGDISFYNAVDGSHIHTFLDVSFSEALYPVFRILTLEPTALT
ICPAGGGGSGGGGSGGGGSWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Sequence of entity 2 (B), FASTA

>9JQR_2 Butyrophilin subfamily 3 member A2 (chains B)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSN
LHVEVKGYEDGGIHLECRSTGWYPQPQIQWSNAKGENIPAVEAPVVADGVGLYEVAASVI
MRGGSGEGVSCIIRNSLLGLEKTASISIADPFFRSAQPWIAALAGTLPILLLLLAGASYF
LWRQQKEITALSSEIESEQEMKEMGYAATEREISLRESLQEELKRKKIQYLTRGEESSSD
TNKSAGGGGSDYKDDDDK

Sequence of entity 3 (D), FASTA

>9JQR_3 Vdelta2 T cell receptor (chains D)
AIELVPEHQTVPVSIGVPATLRCSMKGEAIGNYYINWYRKTQGNTMTFIYREKDIYGPGF
KDNFQGDIDIAKNLAVLKILAPSERDEGSYYCACDTLGMGGEYTDKLIFGKGTRVTVEPR
SQPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKL
GKYEDSNSVTCSVQHDNKTVHSTDFEVKTDSTDHVKPKETENTKQPSKSSSADLVPRGST
TAPSAQLEKELQALEKENAQLEWELQALEKELAQ

Sequence of entity 4 (E, F), FASTA

>9JQR_4 Butyrophilin subfamily 2 member A1 (chains E, F)
QFIVVGPTDPILATVGENTTLRCHLSPEKNAEDMEVRWFRSQFSPAVFVYKGGRERTEEQ
MEEYRGRTTFVSKDISRGSVALVIHNITAQENGTYRCYFQEGRSYDEAILHLVVAGLGSK
PLISMRGHEDGGIRLECISRGWYPKPLTVWRDPYGGVAPALKEVSMPDADGLFMVTTAVI
IRDKSVRNMSCSINNTLLGQKKESVIFIPESFMPSVSPCAVALPIIVVILMIPIAVCIYW
INKLQKEKKILSGEKEFERETREIALKELEKERVQKEEELQVKEKLQEELRWRRTFLHAV
DVVLDPDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNPERFDSQPCVLGRESFASGKHYW
EVEVENVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEMHKGQYRAVSSPDRILPLKESLC
RVGVFLDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRPFFRLGCEDSPIFICPALTGANG
VTVPEEGLTLHRVGTHQSLGGGGSWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Sequence of entity 5 (G), FASTA

>9JQR_5 Vgamma9 T cell receptor (chains G)
AGHLEQPQISSTKTLSKTARLECVVSGITISATSVYWYRERPGEVIQFLVSISYDGTVRK
ESGIPSGKFEVDRIPETSTSTLTIHNVEKQDIATYYCALWEAQQELGKKIKVFGPGTKLI
ITDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDVIKIHWEEKKSNTILGSQ
EGNTMKTNDTYMKFSWLTVPEKSLDKEHRCIVRHENNKNGVDQEIIFPPIKTDVITMDPK
DNSSADLVPRGSTTAPSAQLKKKLQALKKKNAQLKWKLQALKKKLAQHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9
H6P	(2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate	C5 H12 O8 P2	1

Primary citation

Structures of butyrophilin multimers reveal a plier-like mechanism for V gamma 9V delta 2 T cell receptor activation. Zhang, M., Wang, Y., Cai, N. et al. Immunity (2025) 58:1660. DOI 10.1016/j.immuni.2025.05.011 · PubMed

Other PDB entries of the same protein (UniProt O00481 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ITA 1.2 Å, Crystal structure of intracellular B30.2 domain of BTN3A1 mutant
6ISM 1.25 Å, Crystal structure of intracellular B30.2 domain of BTN3A1 mutant
8IZE 1.4 Å, Crystal structure of intracellular B30.2 domain of BTN3A1 in complex with 4-HMBPP
4N7I 1.4 Å, Crystal Structure of Intracellular B30.2 Domain of BTN3A1
4N7U 1.46 Å, Crystal Structure of Intracellular B30.2 Domain of BTN3A1 in Complex with CHDMAPP
5LYG 1.6 Å, Crystal structure of intracellular B30.2 domain of BTN3A1 bound to malonate
8IZG 1.6 Å, Crystal structure of intracellular B30.2 domain of BTN3A1 in complex with 5-HMBPP
5LYK 1.7 Å, Crystal structure of intracellular B30.2 domain of BTN3A1 bound to citrate
8IXV 1.72 Å, Crystal structure of intracellular B30.2 domain of BTN3A in complex with 2Cl-HMBPP
4K55 1.91 Å, Structure of the extracellular domain of butyrophilin BTN3A1 in complex with…
5HM7 1.93 Å, The Intracellular domain of Butyrophilin 3A1 protein
4F80 1.94 Å, Crystal Structure of the human BTN3A1 ectodomain

Browse structure collections

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