9II6: Intracellular domains of BTN2A1-BTN3A1-BTN3A3

Cryo-EM structure of the intracellular domains of BTN2A1-BTN3A1-BTN3A3. Determined by electron microscopy at 3.27 Å resolution. Released 25 Jun 2025.

Method: Electron microscopy
Resolution: 3.27 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,975
Mol. weight: 122.74 kDa
Ligands: H6P
Released: 25 Jun 2025

Explore 9II6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9II6 contains 14 α-helices and 67 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 A: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	247-261	15
α-helix	263-292	30
β-strand	297-299	3	1
β-strand	304	1	2
β-strand	313-315	3	1
β-strand	321-324	4	1
β-strand	346-348	3	3
β-strand	349	1	2
β-strand	353	1	3
β-strand	357-363	7	1
β-strand	370-376	7	3
β-strand	393-399	7	3
β-strand	402-404	3	3
β-strand	412	1	3
β-strand	421-427	7	1
β-strand	432-437	6	1
β-strand	442-446	5	1
α-helix	447-449	3
β-strand	456-462	7	3
β-strand	469-471	3	1
α-helix	472-475	4
β-strand	488-489	2	1

Chain B: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	247-290	44
α-helix	300-307	8
β-strand	309-310	2	4
α-helix	317-319	3
β-strand	324-326	3	5
β-strand	333-335	3	5
β-strand	354-356	3	6
β-strand	361	1	6
β-strand	365-371	7	4
β-strand	378-384	7	6
β-strand	401-407	7	6
β-strand	411-414	4	6
β-strand	420-421	2	6
β-strand	430-436	7	4
β-strand	441-446	6	4
β-strand	452-456	5	4
β-strand	465-470	6	6
β-strand	479	1	5
β-strand	480-481	2	4

Chain D: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	247-292	46
α-helix	300-307	8
β-strand	309	1	7
β-strand	315	1	8
α-helix	317-319	3
β-strand	324-326	3	9
β-strand	333-335	3	9
β-strand	354-355	2	10
β-strand	357	1	8
β-strand	361	1	10
β-strand	365-371	7	7
β-strand	377-384	8	10
β-strand	402-408	7	10
β-strand	412-415	4	10
β-strand	422-423	2	10
β-strand	431-437	7	7
β-strand	442-447	6	7
β-strand	452-456	5	7
β-strand	466-471	6	10
β-strand	480	1	9
β-strand	481-482	2	7

Chain E: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	247-252	6
α-helix	255-293	39
β-strand	297-299	3	1
β-strand	313-315	3	1
β-strand	321-324	4	1
β-strand	346-348	3	11
β-strand	353	1	11
β-strand	357-363	7	1
β-strand	370-376	7	11
β-strand	393-399	7	11
β-strand	402-404	3	11
β-strand	421-427	7	1
β-strand	432-437	6	1
β-strand	442-446	5	1
α-helix	447-449	3
β-strand	456-462	7	11
β-strand	469-471	3	1
α-helix	472-475	4
β-strand	488-489	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Butyrophilin subfamily 2 member A1	A, E	protein	254	Homo sapiens	Q7KYR7 (AlphaFold model)
Butyrophilin subfamily 3 member A1	B	protein	239	Homo sapiens	O00481 (AlphaFold model)
Butyrophilin subfamily 3 member A3	D	protein	310	Homo sapiens	O00478 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>9II6_1 Butyrophilin subfamily 2 member A1 (chains A, E)
KEKKILSGEKEFERETREIALKELEKERVQKEEELQVKEKLQEELRWRRTFLHAVDVVLD
PDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNPERFDSQPCVLGRESFASGKHYWEVEVE
NVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEMHKGQYRAVSSPDRILPLKESLCRVGVF
LDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRPFFRLGCEDSPIFICPALTGANGVTVPE
EGLTLHRVGTHQSL

Sequence of entity 2 (B), FASTA

>9II6_2 Butyrophilin subfamily 3 member A1 (chains B)
EEKKTQFRKKKREQELREMAWSTMKQEQSTRVKLLEELRWRSIQYASRGERHSAYNEWKK
ALFKPADVILDPKTANPILLVSEDQRSVQRAKEPQDLPDNPERFNWHYCVLGCESFISGR
HYWEVEVGDRKEWHIGVCSKNVQRKGWVKMTPENGFWTMGLTDGNKYRTLTEPRTNLKLP
KTPKKVGVFLDYETGDISFYNAVDGSHIHTFLDVSFSEALYPVFRILTLEPTALTICPA

Sequence of entity 3 (D), FASTA

>9II6_3 Butyrophilin subfamily 3 member A3 (chains D)
KEKIALSRETEREREMKEMGYAATEQEISLREKLQEELKWRKIQYMARGEKSLAYHEWKM
ALFKPADVILDPDTANAILLVSEDQRSVQRAEEPRDLPDNPERFEWRYCVLGCENFTSGR
HYWEVEVGDRKEWHIGVCSKNVERKKGWVKMTPENGYWTMGLTDGNKYRALTEPRTNLKL
PEPPRKVGIFLDYETGEISFYNATDGSHIYTFPHASFSEPLYPVFRILTLEPTALTICPI
PKEVESSPDPDLVPDHSLETPLTPGLANESGEPQAEVTSLLLPAHPGAEVSPSATTNQNH
KLQARTEALY

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
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…
8ZJX 3.35 Å, Cryo-EM structure of the full length pAg-bound BTN2A1-BTN3A1-BTN3A2 in complex with…

Browse structure collections

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