9J5J: BTN2A1-BTN3A1-BTN3A2

Cryo-EM structure of BTN2A1-BTN3A1-BTN3A2 in complex with gdTCR. Determined by electron microscopy at 4.05 Å resolution. Released 21 May 2025.

Method: Electron microscopy
Resolution: 4.05 Å
Organism: Homo sapiens
Chains: 8
Atoms: 20,297
Mol. weight: 300.87 kDa
Ligands: H6P
Released: 21 May 2025

Explore 9J5J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9J5J contains 45 α-helices and 210 β-strands across 8 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: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-14	5	2
β-strand	19-26	8	1
α-helix	30-32	3
β-strand	35-40	6	2
β-strand	47-51	5	2
β-strand	55-56	2	2
β-strand	64-69	6	1
β-strand	74-79	6	1
β-strand	88-95	8	2
β-strand	107-109	3	2
α-helix	110-111	2
β-strand	113-118	6	2
α-helix	126-127	2
β-strand	128-134	7	3
β-strand	137-145	9	3
β-strand	151-155	5	4
β-strand	159-162	4	3
β-strand	166-169	4	3
β-strand	175-183	9	3
α-helix	186-188	3
β-strand	190-195	6	4
β-strand	198-200	3	4
α-helix	202-205	4

Chain B: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	5
β-strand	10-13	4	6
β-strand	18-26	9	5
β-strand	35-40	6	6
β-strand	47-52	6	6
β-strand	58-60	3	6
β-strand	69-74	6	5
β-strand	79-85	7	5
α-helix	89-91	3
β-strand	93-102	10	6
β-strand	109-113	5	6
β-strand	117-121	5	6
β-strand	133-137	5	7
α-helix	138-140	3
α-helix	141-147	7
β-strand	150-157	8	7
β-strand	165-170	6	8
α-helix	175	1
β-strand	176	1	8
α-helix	177	1
β-strand	180-187	8	7
β-strand	190-199	10	7
α-helix	201-203	3
β-strand	208-213	6	8
α-helix	218-220	3
α-helix	221-222	2
β-strand	223-227	5	8

Chain C: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	9
β-strand	11-13	3	10
β-strand	19-23	5	11
β-strand	24-26	3	9
β-strand	35-40	6	10
β-strand	45-51	7	10
β-strand	54-55	2	10
β-strand	68-74	7	11
β-strand	79-84	6	11
β-strand	93-101	9	10
β-strand	104-114	11	10
β-strand	116	1	12
β-strand	122-129	8	13
β-strand	132-142	11	13
β-strand	143	1	12
β-strand	147-151	5	14
β-strand	161-162	2	13
β-strand	167	1	13
β-strand	173-181	9	13
β-strand	190-195	6	14
β-strand	200-207	8	14
α-helix	211-213	3
α-helix	218-302	85

Chain D: 5 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	15
α-helix	10	1
β-strand	11-13	3	16
β-strand	19-23	5	17
β-strand	24-26	3	15
β-strand	35-40	6	16
β-strand	46-51	6	16
β-strand	54-55	2	16
β-strand	68-71	4	17
β-strand	80-84	5	17
α-helix	89-91	3
β-strand	93-101	9	16
β-strand	104-114	11	16
β-strand	116	1	18
β-strand	122-129	8	14
β-strand	132-142	11	14
β-strand	143	1	18
β-strand	147-151	5	13
β-strand	157	1	13
β-strand	161-162	2	14
β-strand	166-167	2	14
β-strand	173-181	9	14
β-strand	189-195	7	13
β-strand	200-207	8	13
α-helix	210-213	4
α-helix	219-289	71
α-helix	297-306	10
β-strand	309-310	2	19
β-strand	315	1	20
β-strand	324-326	3	19
β-strand	332-335	4	19
β-strand	354-356	3	21
β-strand	357	1	20
β-strand	361	1	21
β-strand	365-371	7	19
β-strand	378-384	7	21
β-strand	401-407	7	21
β-strand	411-414	4	21
β-strand	420-421	2	21
β-strand	430-436	7	19
β-strand	441-446	6	19
β-strand	452-456	5	19
β-strand	465-470	6	21
β-strand	479-482	4	19

Chain E: 8 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	22
β-strand	11-14	4	23
β-strand	19-23	5	24
β-strand	24-25	2	22
β-strand	34-39	6	25
β-strand	48-52	5	25
β-strand	54	1	25
β-strand	68-71	4	24
β-strand	80-84	5	24
α-helix	89-91	3
β-strand	94-100	7	25
β-strand	105-111	7	25
β-strand	112-115	4	23
β-strand	116	1	26
α-helix	119-121	3
β-strand	122-129	8	27
β-strand	132-142	11	27
β-strand	143	1	26
β-strand	147-151	5	28
β-strand	157-158	2	28
β-strand	162-167	6	27
β-strand	173-181	9	27
β-strand	188-194	7	28
β-strand	201-207	7	28
α-helix	222-292	71
β-strand	297-299	3	29
α-helix	306-308	3
β-strand	313-315	3	29
β-strand	321-324	4	29
β-strand	346-348	3	30
β-strand	357-363	7	29
β-strand	370-376	7	30
α-helix	384-385	2
α-helix	389-391	3
β-strand	394-399	6	30
β-strand	402-403	2	30
β-strand	404	1	31
β-strand	412	1	31
β-strand	421-427	7	29
β-strand	432-437	6	29
β-strand	442-446	5	29
α-helix	447-449	3
β-strand	456-462	7	30
β-strand	469-471	3	29
α-helix	472-474	3
β-strand	489	1	32

Chain G: 10 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	33
β-strand	19-23	5	34
β-strand	36-39	4	35
β-strand	49-50	2	35
β-strand	69-70	2	34
α-helix	76-78	3
β-strand	80-84	5	34
α-helix	89-91	3
β-strand	93-95	3	33
β-strand	96-99	4	35
β-strand	106-107	2	35
β-strand	110-115	6	33
α-helix	120-121	2
β-strand	122-129	8	36
β-strand	132-139	8	36
β-strand	147-151	5	37
α-helix	156	1
β-strand	157	1	37
α-helix	158-160	3
β-strand	162-167	6	36
β-strand	173-181	9	36
β-strand	188-194	7	37
β-strand	201-207	7	37
α-helix	219-229	11
α-helix	231-292	62
β-strand	304	1	38
β-strand	313-314	2	39
β-strand	321-322	2	40
β-strand	323-324	2	39
α-helix	334-336	3
β-strand	346-347	2	41
β-strand	349	1	38
β-strand	353	1	41
β-strand	357-363	7	32
β-strand	371-376	6	41
β-strand	393-399	7	41
β-strand	402-404	3	41
β-strand	412-413	2	41
β-strand	421-427	7	32
β-strand	432-437	6	32
β-strand	442-446	5	32
α-helix	447-449	3
β-strand	456-461	6	41
β-strand	469-470	2	40
α-helix	472-474	3
β-strand	489	1	29

Chain H: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	42
β-strand	21-22	2	43
β-strand	33-40	8	42
β-strand	47-51	5	42
β-strand	55-56	2	42
β-strand	66-69	4	43
β-strand	74-77	4	43
β-strand	88-96	9	42
β-strand	108-109	2	42
β-strand	113-116	4	42
α-helix	122-124	3
β-strand	130-133	4	44
β-strand	137-145	9	44
β-strand	153	1	45
β-strand	161	1	44
β-strand	166-169	4	44
β-strand	175-182	8	44
α-helix	186-188	3
β-strand	192	1	45
β-strand	193	1	46
β-strand	200	1	46

Chain I: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	47
β-strand	10-14	5	48
β-strand	19-26	8	47
β-strand	35-40	6	48
β-strand	46-52	7	48
β-strand	58-60	3	48
α-helix	65	1
β-strand	69-74	6	47
β-strand	79-84	6	47
α-helix	89-91	3
β-strand	94-102	9	48
β-strand	109-112	4	48
β-strand	117-122	6	48
β-strand	133-135	3	49
α-helix	142-145	4
β-strand	154-159	6	49
β-strand	165-170	6	50
β-strand	180-181	2	49
β-strand	185-187	3	49
β-strand	190-196	7	49
α-helix	202-204	3
β-strand	208-213	6	50
α-helix	218-220	3
β-strand	223-227	5	50

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
d domain of gdTCR	A, H	protein	205	Homo sapiens
g domain of gdTCR	B, I	protein	230	Homo sapiens	P0CF51 (AlphaFold model)
Butyrophilin subfamily 3 member A2	C	protein	305	Homo sapiens	P78410 (AlphaFold model)
Butyrophilin subfamily 3 member A1	D	protein	484	Homo sapiens	O00481 (AlphaFold model)
Butyrophilin subfamily 2 member A1	E, G	protein	499	Homo sapiens	Q7KYR7 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>9J5J_1 d domain of gdTCR (chains A, H)
IELVPEHQTVPVSIGVPATLRCSMKGEAIGNYYINWYRKTQGNTMTFIYREKDIYGPGFK
DNFQGDIDIAKNLAVLKILAPSERDEGSYYCASDTLGMGGEYTDKLIFGKGTRVTVEPRS
QPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLG
KYEDSNSVTCSVQHDNKTVHSTDFE

Sequence of entity 2 (B, I), FASTA

>9J5J_2 g domain of gdTCR (chains B, I)
GHLEQPQISSTKTLSKTARLECVVSGITISATSVYWYRERPGEVIQFLVSISYDGTVRKE
SGIPSGKFEVDRIPETSTSTLTIHNVEKQDIATYYCALWEAQQELGKKIKVFGPGTKLII
TDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILGSQE
GNTMKTNDTYMKFSWLTVPEESLDKEHRCIVRHENNKNGVDQEIIFPPIK

Sequence of entity 3 (C), FASTA

>9J5J_3 Butyrophilin subfamily 3 member A2 (chains C)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSN
LHVEVKGYEDGGIHLECRSTGWYPQPQIQWSNAKGENIPAVEAPVVADGVGLYEVAASVI
MRGGSGEGVSCIIRNSLLGLEKTASISIADPFFRSAQPWIAALAGTLPILLLLLAGASYF
LWRQQKEITALSSEIESEQEMKEMGYAATEREISLRESLQEELKRKKIQYLTRGEESSSD
TNKSA

Sequence of entity 4 (D), FASTA

>9J5J_4 Butyrophilin subfamily 3 member A1 (chains D)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSD
LHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVI
MRGSSGEGVSCTIRSSLLGLEKTASISIADPFFRSAQRWIAALAGTLPVLLLLLGGAGYF
LWQQQEEKKTQFRKKKREQELREMAWSTMKQEQSTRVKLLEELRWRSIQYASRGERHSAY
NEWKKALFKPADVILDPKTANPILLVSEDQRSVQRAKEPQDLPDNPERFNWHYCVLGCES
FISGRHYWEVEVGDRKEWHIGVCSKNVQRKGWVKMTPENGFWTMGLTDGNKYRTLTEPRT
NLKLPKTPKKVGVFLDYETGDISFYNAVDGSHIHTFLDVSFSEALYPVFRILTLEPTALT
ICPA

Sequence of entity 5 (E, G), FASTA

>9J5J_5 Butyrophilin subfamily 2 member A1 (chains E, G)
QFIVVGPTDPILATVGENTTLRCHLSPEKNAEDMEVRWFRSQFSPAVFVYKGGRERTEEQ
MEEYRGRTTFVSKDISRGSVALVIHNITAQENGTYRCYFQEGRSYDEAILHLVVAGLGSK
PLISMRGHEDGGIRLECISRGWYPKPLTVWRDPYGGVAPALKEVSMPDADGLFMVTTAVI
IRDKSVRNMSCSINNTLLGQKKESVIFIPESFMPSVSPCAVALPIIVVILMIPIAVCIYW
INKLQKEKKILSGEKEFERETREIALKELEKERVQKEEELQVKEKLQEELRWRRTFLHAV
DVVLDPDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNPERFDSQPCVLGRESFASGKHYW
EVEVENVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEMHKGQYRAVSSPDRILPLKESLC
RVGVFLDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRPFFRLGCEDSPIFICPALTGANG
VTVPEEGLTLHRVGTHQSL

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-induced inside-out stabilization of butyrophilin receptor complexes drives dimerization-dependent gamma delta TCR activation. Zhu, Y., Gao, W., Zheng, J. et al. Immunity (2025) 58:1646. DOI 10.1016/j.immuni.2025.04.012 · PubMed

Other PDB entries of the same protein (UniProt P0CF51 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LFH 2.3 Å, Crystal Structure of 9C2 TCR
4LHU 2.87 Å, Crystal Structure of 9C2 TCR bound to CD1d
9CI8 3.01 Å, T cell receptor complex
8JBV 3.02 Å, Extracellular domain of gamma delta TCR
9JY1 3.08 Å, delta epsilon/delta epsilon Fab-TCR tetramer
9JY2 3.24 Å, Fab-CD3-delta epsilon-TCR complex
9JY4 3.29 Å, gamma epsilon/gamma epsilon Fab-TCR tetramer
9JXZ 3.31 Å, V gamma9 V delta2 TCR and CD3 complex
9JY3 3.35 Å, delta epsilon/gamma epsilon Fab-TCR tetramer
9CIA 3.39 Å, T cell receptor complex
8JC0 3.4 Å, V gamma9 V delta2 TCR and CD3 complex in LMNG
9JY0 3.69 Å, Fab-CD3-gamma epsilon-TCR complex

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