9IIK: BTN2A1-BTN3A1-BTN3A2

Cryo-EM structure of BTN2A1-BTN3A1-BTN3A2. Determined by electron microscopy at 4.12 Å resolution. Released 25 Jun 2025.

Method: Electron microscopy
Resolution: 4.12 Å
Organism: Homo sapiens
Chains: 4
Atoms: 14,001
Mol. weight: 201.67 kDa
Ligands: H6P
Released: 25 Jun 2025

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

Secondary structure: helices and β-sheets

9IIK contains 25 α-helices and 140 β-strands across 4 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 C: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	22
α-helix	10	1
β-strand	11-14	4	23
β-strand	19-23	5	24
β-strand	24-26	3	22
β-strand	35-40	6	23
β-strand	46-51	6	23
β-strand	54-55	2	23
α-helix	57-59	3
α-helix	62-64	3
β-strand	68-74	7	24
β-strand	79-84	6	24
α-helix	89-91	3
β-strand	93-101	9	23
β-strand	104-115	12	23
β-strand	116	1	25
α-helix	117-121	5
β-strand	122-129	8	26
β-strand	132-142	11	26
β-strand	143	1	25
β-strand	147-151	5	27
β-strand	157-158	2	27
β-strand	161-162	2	26
α-helix	163-165	3
β-strand	166-167	2	26
β-strand	173-181	9	26
β-strand	189-195	7	27
β-strand	200-207	8	27
α-helix	210-214	5
α-helix	217-304	88

Chain D: 6 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	28
α-helix	10	1
β-strand	11-14	4	29
β-strand	19-23	5	30
β-strand	24-26	3	28
β-strand	35-40	6	29
β-strand	45-51	7	29
β-strand	54-56	3	29
β-strand	68-74	7	30
β-strand	79-84	6	30
β-strand	93-101	9	29
β-strand	104-115	12	29
β-strand	116	1	31
β-strand	122-129	8	27
β-strand	132-142	11	27
β-strand	143	1	31
β-strand	147-151	5	26
β-strand	157-158	2	26
β-strand	161-162	2	27
α-helix	163-165	3
β-strand	166-167	2	27
β-strand	173-181	9	27
β-strand	189-195	7	26
β-strand	200-208	9	26
α-helix	210-212	3
α-helix	216-219	4
α-helix	220-292	73
α-helix	297-307	11
β-strand	310	1	32
β-strand	315	1	33
β-strand	324-326	3	32
β-strand	332-335	4	32
β-strand	354-356	3	34
β-strand	357	1	33
β-strand	361	1	34
β-strand	365-371	7	32
β-strand	378-384	7	34
β-strand	401-407	7	34
β-strand	411-414	4	34
β-strand	420-421	2	34
β-strand	430-436	7	32
β-strand	441-446	6	32
β-strand	452-456	5	32
β-strand	465-470	6	34
β-strand	479-480	2	32

Chain E: 8 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
α-helix	10-11	2
β-strand	12	1	2
β-strand	21-23	3	3
β-strand	24-26	3	1
β-strand	35-39	5	4
β-strand	46	1	5
β-strand	48-51	4	4
β-strand	54-56	3	4
β-strand	60	1	5
α-helix	62-64	3
β-strand	68-71	4	3
β-strand	80-84	5	3
α-helix	89-91	3
β-strand	93-101	9	4
β-strand	104-112	9	4
β-strand	113	1	2
α-helix	118-121	4
β-strand	122	1	6
β-strand	134	1	7
β-strand	138-142	5	6
β-strand	147-151	5	8
β-strand	157	1	8
β-strand	162-167	6	6
β-strand	173-178	6	6
β-strand	180	1	7
β-strand	188-194	7	8
β-strand	201-207	7	8
α-helix	219-289	71
β-strand	297-299	3	9
β-strand	304-305	2	10
α-helix	306-308	3
β-strand	313-315	3	9
β-strand	321-324	4	9
β-strand	346-349	4	10
β-strand	353	1	10
β-strand	357-363	7	9
β-strand	370-376	7	10
α-helix	389-391	3
β-strand	393-397	5	10
β-strand	399	1	11
β-strand	402	1	11
β-strand	421-427	7	9
β-strand	432-437	6	9
β-strand	442-446	5	9
β-strand	456-462	7	10
β-strand	469-471	3	9
α-helix	472-474	3
β-strand	489	1	9

Chain G: 3 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	12
β-strand	11-13	3	13
β-strand	24	1	12
β-strand	35-39	5	13
β-strand	48-50	3	13
β-strand	68-71	4	14
β-strand	81-84	4	14
β-strand	93-100	8	13
β-strand	105-114	10	13
β-strand	116	1	15
β-strand	122-129	8	16
β-strand	132-142	11	16
β-strand	143	1	15
β-strand	147-151	5	17
β-strand	162-167	6	16
α-helix	172	1
β-strand	173-179	7	16
β-strand	188-194	7	17
β-strand	201-207	7	17
α-helix	222-252	31
α-helix	255-294	40
β-strand	297-299	3	9
β-strand	304-305	2	18
β-strand	313-314	2	19
β-strand	321-322	2	9
β-strand	323-324	2	19
β-strand	346-349	4	18
β-strand	353	1	18
β-strand	357-363	7	9
β-strand	371-376	6	18
β-strand	393-397	5	18
β-strand	398	1	20
β-strand	403	1	20
β-strand	404	1	21
β-strand	412	1	21
β-strand	421-427	7	9
β-strand	432-437	6	9
β-strand	442-446	5	9
β-strand	456-461	6	18
β-strand	469-471	3	9
β-strand	488	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Butyrophilin subfamily 2 member A1	E, G	protein	499	Homo sapiens	Q7KYR7 (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)

Sequence of entity 1 (E, G), FASTA

>9IIK_1 Butyrophilin subfamily 2 member A1 (chains E, G)
QFIVVGPTDPILATVGENTTLRCHLSPEKNAEDMEVRWFRSQFSPAVFVYKGGRERTEEQ
MEEYRGRTTFVSKDISRGSVALVIHNITAQENGTYRCYFQEGRSYDEAILHLVVAGLGSK
PLISMRGHEDGGIRLECISRGWYPKPLTVWRDPYGGVAPALKEVSMPDADGLFMVTTAVI
IRDKSVRNMSCSINNTLLGQKKESVIFIPESFMPSVSPCAVALPIIVVILMIPIAVCIYW
INKLQKEKKILSGEKEFERETREIALKELEKERVQKEEELQVKEKLQEELRWRRTFLHAV
DVVLDPDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNPERFDSQPCVLGRESFASGKHYW
EVEVENVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEMHKGQYRAVSSPDRILPLKESLC
RVGVFLDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRPFFRLGCEDSPIFICPALTGANG
VTVPEEGLTLHRVGTHQSL

Sequence of entity 2 (C), FASTA

>9IIK_2 Butyrophilin subfamily 3 member A2 (chains C)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSN
LHVEVKGYEDGGIHLECRSTGWYPQPQIQWSNAKGENIPAVEAPVVADGVGLYEVAASVI
MRGGSGEGVSCIIRNSLLGLEKTASISIADPFFRSAQPWIAALAGTLPILLLLLAGASYF
LWRQQKEITALSSEIESEQEMKEMGYAATEREISLRESLQEELKRKKIQYLTRGEESSSD
TNKSA

Sequence of entity 3 (D), FASTA

>9IIK_3 Butyrophilin subfamily 3 member A1 (chains D)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSD
LHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVI
MRGSSGEGVSCTIRSSLLGLEKTASISIADPFFRSAQRWIAALAGTLPVLLLLLGGAGYF
LWQQQEEKKTQFRKKKREQELREMAWSTMKQEQSTRVKLLEELRWRSIQYASRGERHSAY
NEWKKALFKPADVILDPKTANPILLVSEDQRSVQRAKEPQDLPDNPERFNWHYCVLGCES
FISGRHYWEVEVGDRKEWHIGVCSKNVQRKGWVKMTPENGFWTMGLTDGNKYRTLTEPRT
NLKLPKTPKKVGVFLDYETGDISFYNAVDGSHIHTFLDVSFSEALYPVFRILTLEPTALT
ICPA

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) 58:1646-1659.e5. DOI 10.1016/j.immuni.2025.04.012 · 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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