9J5M: Ectodomain of BTN2A1-BTN3A1-BTN3A2

Cryo-EM structure of the ectodomain of BTN2A1-BTN3A1-BTN3A2 in complex with gdTCR. Determined by electron microscopy at 3.94 Å resolution. Released 21 May 2025.

Method: Electron microscopy
Resolution: 3.94 Å
Organism: Homo sapiens
Chains: 8
Atoms: 12,892
Mol. weight: 299.27 kDa
Released: 21 May 2025

Explore 9J5M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9J5M contains 34 α-helices and 173 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, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	10-14	5	2
β-strand	19-23	5	3
β-strand	24-26	3	1
β-strand	35-40	6	2
β-strand	47-51	5	2
β-strand	55-56	2	2
α-helix	60-63	4
β-strand	64-69	6	3
β-strand	74-79	6	3
β-strand	88-94	7	2
β-strand	99	1	4
β-strand	102	1	4
β-strand	108	1	2
β-strand	113-118	6	2
α-helix	119-121	3
β-strand	128-134	7	5
β-strand	137-145	9	5
β-strand	152-155	4	6
β-strand	161-162	2	5
α-helix	164-165	2
β-strand	166-169	4	5
β-strand	175-182	8	5
α-helix	186-188	3
β-strand	190-195	6	6
β-strand	198-200	3	6
α-helix	202-205	4

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	7
β-strand	10-13	4	8
β-strand	18-26	9	7
β-strand	35-40	6	8
β-strand	47-52	6	8
β-strand	58-59	2	8
α-helix	64-65	2
β-strand	69-74	6	7
β-strand	79-85	7	7
α-helix	89-91	3
β-strand	93-102	10	8
β-strand	109-113	5	8
β-strand	117-121	5	8
α-helix	132	1
β-strand	133-137	5	9
α-helix	138-140	3
α-helix	141-144	4
β-strand	149-150	2	10
β-strand	153-157	5	9
β-strand	165-170	6	11
α-helix	175	1
β-strand	176	1	11
α-helix	177-178	2
β-strand	180-181	2	9
β-strand	185-187	3	9
β-strand	190-196	7	9
β-strand	199-200	2	10
β-strand	208-213	6	11
α-helix	218-220	3
β-strand	223	1	11
β-strand	226-227	2	11
α-helix	228-229	2

Chain C: 2 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	12
β-strand	11-13	3	13
β-strand	19	1	14
β-strand	22-23	2	14
β-strand	24-26	3	12
β-strand	35-40	6	13
β-strand	45-51	7	13
β-strand	54-56	3	13
β-strand	68-71	4	14
β-strand	80-84	5	14
α-helix	89-91	3
β-strand	93-100	8	13
β-strand	109-114	6	13
β-strand	116	1	15
β-strand	122-129	8	16
β-strand	132-138	7	16
β-strand	139-142	4	17
β-strand	143	1	15
β-strand	147-151	5	18
β-strand	157	1	18
β-strand	161-162	2	16
β-strand	173-175	3	17
β-strand	177-181	5	16
β-strand	189-195	7	18
β-strand	200-207	8	18
α-helix	211-213	3

Chain D: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	19
α-helix	10	1
β-strand	11-13	3	20
β-strand	22-26	5	19
β-strand	35-39	5	21
β-strand	46-51	6	21
β-strand	54-56	3	21
α-helix	62-64	3
β-strand	68-74	7	19
β-strand	79-84	6	19
β-strand	93-94	2	20
β-strand	97-101	5	21
β-strand	104-106	3	21
β-strand	111-114	4	20
β-strand	121-129	9	18
β-strand	132-142	11	18
β-strand	147-151	5	16
β-strand	157	1	16
β-strand	161-162	2	18
α-helix	163-165	3
β-strand	166-167	2	18
β-strand	173-181	9	18
β-strand	189-194	6	16
β-strand	201-207	7	16
α-helix	210-213	4

Chain E: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	22
β-strand	11-14	4	23
β-strand	19-23	5	24
β-strand	24-26	3	22
β-strand	35-39	5	25
β-strand	48-51	4	25
α-helix	62-64	3
β-strand	68-71	4	24
β-strand	80-84	5	24
β-strand	94-98	5	25
β-strand	107-111	5	25
β-strand	112-115	4	23
β-strand	116	1	26
α-helix	119-121	3
β-strand	122	1	27
β-strand	125-128	4	28
β-strand	133-135	3	28
β-strand	138-142	5	27
β-strand	143	1	26
β-strand	147-151	5	29
α-helix	156	1
β-strand	157-158	2	29
α-helix	159	1
β-strand	162-167	6	27
β-strand	173-178	6	27
β-strand	179-181	3	28
β-strand	188	1	30
β-strand	191-194	4	29
β-strand	201-202	2	29
β-strand	207	1	30

Chain G: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	31
β-strand	11-14	4	32
β-strand	19-25	7	31
β-strand	36-39	4	32
β-strand	48-50	3	32
β-strand	69-71	3	31
α-helix	76-78	3
β-strand	79-84	6	31
α-helix	89-91	3
β-strand	93-99	7	32
β-strand	107-115	9	32
β-strand	122-128	7	33
β-strand	133-140	8	33
β-strand	147-151	5	34
β-strand	157	1	34
β-strand	162-167	6	33
β-strand	173-181	9	33
β-strand	188-194	7	34
β-strand	201-207	7	34

Chain H: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	35
β-strand	10-12	3	36
β-strand	21-22	2	37
β-strand	26	1	35
β-strand	33-40	8	36
β-strand	47-51	5	36
β-strand	55-56	2	36
β-strand	66-69	4	37
β-strand	74-77	4	37
β-strand	88-96	9	36
β-strand	108-109	2	36
α-helix	111-112	2
β-strand	113-116	4	36
α-helix	122-124	3
β-strand	130-133	4	38
β-strand	137-143	7	38
β-strand	153	1	39
β-strand	161	1	38
β-strand	166-169	4	38
β-strand	175-182	8	38
β-strand	192	1	39

Chain I: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	40
β-strand	10-14	5	41
β-strand	19-26	8	40
β-strand	35-40	6	41
β-strand	46-52	7	41
β-strand	58-60	3	41
β-strand	62	1	42
β-strand	64	1	42
α-helix	65	1
β-strand	69-74	6	40
β-strand	79-84	6	40
α-helix	89-91	3
β-strand	94-102	9	41
β-strand	109-113	5	41
β-strand	117-122	6	41
β-strand	133-135	3	43
α-helix	142-145	4
β-strand	154-157	4	43
β-strand	165-170	6	44
β-strand	180-181	2	43
β-strand	185-187	3	43
β-strand	190-196	7	43
α-helix	203-205	3
β-strand	208-213	6	44
α-helix	218-220	3
α-helix	221-222	2
β-strand	223-227	5	44

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
d subunit of gdTCR	A, H	protein	205	Homo sapiens
g subunit 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

>9J5M_1 d subunit of gdTCR (chains A, H)
IELVPEHQTVPVSIGVPATLRCSMKGEAIGNYYINWYRKTQGNTMTFIYREKDIYGPGFK
DNFQGDIDIAKNLAVLKILAPSERDEGSYYCASDTLGMGGEYTDKLIFGKGTRVTVEPRS
QPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLG
KYEDSNSVTCSVQHDNKTVHSTDFE

Sequence of entity 2 (B, I), FASTA

>9J5M_2 g subunit of gdTCR (chains B, I)
GHLEQPQISSTKTLSKTARLECVVSGITISATSVYWYRERPGEVIQFLVSISYDGTVRKE
SGIPSGKFEVDRIPETSTSTLTIHNVEKQDIATYYCALWEAQQELGKKIKVFGPGTKLII
TDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILGSQE
GNTMKTNDTYMKFSWLTVPEESLDKEHRCIVRHENNKNGVDQEIIFPPIK

Sequence of entity 3 (C), FASTA

>9J5M_3 Butyrophilin subfamily 3 member A2 (chains C)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSN
LHVEVKGYEDGGIHLECRSTGWYPQPQIQWSNAKGENIPAVEAPVVADGVGLYEVAASVI
MRGGSGEGVSCIIRNSLLGLEKTASISIADPFFRSAQPWIAALAGTLPILLLLLAGASYF
LWRQQKEITALSSEIESEQEMKEMGYAATEREISLRESLQEELKRKKIQYLTRGEESSSD
TNKSA

Sequence of entity 4 (D), FASTA

>9J5M_4 Butyrophilin subfamily 3 member A1 (chains D)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSD
LHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVI
MRGSSGEGVSCTIRSSLLGLEKTASISIADPFFRSAQRWIAALAGTLPVLLLLLGGAGYF
LWQQQEEKKTQFRKKKREQELREMAWSTMKQEQSTRVKLLEELRWRSIQYASRGERHSAY
NEWKKALFKPADVILDPKTANPILLVSEDQRSVQRAKEPQDLPDNPERFNWHYCVLGCES
FISGRHYWEVEVGDRKEWHIGVCSKNVQRKGWVKMTPENGFWTMGLTDGNKYRTLTEPRT
NLKLPKTPKKVGVFLDYETGDISFYNAVDGSHIHTFLDVSFSEALYPVFRILTLEPTALT
ICPA

Sequence of entity 5 (E, G), FASTA

>9J5M_5 Butyrophilin subfamily 2 member A1 (chains E, G)
QFIVVGPTDPILATVGENTTLRCHLSPEKNAEDMEVRWFRSQFSPAVFVYKGGRERTEEQ
MEEYRGRTTFVSKDISRGSVALVIHNITAQENGTYRCYFQEGRSYDEAILHLVVAGLGSK
PLISMRGHEDGGIRLECISRGWYPKPLTVWRDPYGGVAPALKEVSMPDADGLFMVTTAVI
IRDKSVRNMSCSINNTLLGQKKESVIFIPESFMPSVSPCAVALPIIVVILMIPIAVCIYW
INKLQKEKKILSGEKEFERETREIALKELEKERVQKEEELQVKEKLQEELRWRRTFLHAV
DVVLDPDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNPERFDSQPCVLGRESFASGKHYW
EVEVENVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEMHKGQYRAVSSPDRILPLKESLC
RVGVFLDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRPFFRLGCEDSPIFICPALTGANG
VTVPEEGLTLHRVGTHQSL

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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