9JQQ: HMBPP-primed BTN3A1-BTN3A2-BTN2A1 complex

Cryo-EM structure of the HMBPP-primed BTN3A1-BTN3A2-BTN2A1 complex. Determined by electron microscopy at 3.26 Å resolution. Released 18 Jun 2025.

Method: Electron microscopy
Resolution: 3.26 Å
Organism: Homo sapiens
Chains: 4
Atoms: 13,654
Mol. weight: 215.33 kDa
Ligands: NAG, H6P
Released: 18 Jun 2025

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

Secondary structure: helices and β-sheets

9JQQ contains 28 α-helices and 142 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: 8 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	11-14	4	2
β-strand	19-23	5	3
β-strand	24-26	3	1
β-strand	35-39	5	2
β-strand	48-51	4	2
β-strand	54-55	2	2
α-helix	57-59	3
β-strand	68-71	4	3
α-helix	75-77	3
β-strand	80-84	5	3
β-strand	93-101	9	2
β-strand	104-115	12	2
α-helix	116-118	3
β-strand	122-125	4	4
β-strand	135-138	4	4
β-strand	142	1	5
β-strand	149-151	3	6
β-strand	173	1	5
β-strand	176	1	4
β-strand	189-192	4	6
β-strand	203-207	5	6
α-helix	210-212	3
α-helix	220-289	70
α-helix	297-306	10
β-strand	309-310	2	7
β-strand	315-320	6	8
β-strand	324-326	3	9
β-strand	332-335	4	9
β-strand	354-357	4	8
β-strand	361	1	8
β-strand	365-368	4	7
β-strand	370-371	2	9
β-strand	378-384	7	8
β-strand	401-406	6	8
β-strand	413-414	2	8
β-strand	432-436	5	7
β-strand	441-445	5	7
β-strand	452-455	4	7
α-helix	459-461	3
β-strand	465-470	6	8
β-strand	479-481	3	9
α-helix	482-483	2

Chain B: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	10
α-helix	10	1
β-strand	11-14	4	11
β-strand	19-26	8	10
β-strand	36-40	5	12
α-helix	42-44	3
β-strand	45-50	6	12
α-helix	62-64	3
β-strand	68-71	4	10
β-strand	79-84	6	10
β-strand	94-98	5	12
β-strand	109-111	3	12
β-strand	112-115	4	11
β-strand	122-129	8	6
β-strand	132-142	11	6
α-helix	145-146	2
β-strand	147-151	5	4
β-strand	157-158	2	4
β-strand	161-162	2	6
α-helix	163-165	3
β-strand	173-181	9	6
β-strand	189-195	7	4
β-strand	200-207	8	4
α-helix	218-291	74

Chain E: 7 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	13
α-helix	10	1
β-strand	11	1	14
α-helix	12	1
β-strand	14	1	15
β-strand	19-23	5	16
β-strand	24	1	13
β-strand	35-39	5	14
β-strand	47-50	4	14
β-strand	68-70	3	16
β-strand	80-84	5	16
β-strand	93-100	8	14
β-strand	105-112	8	14
β-strand	115	1	15
β-strand	116	1	17
α-helix	119-121	3
β-strand	122-125	4	18
β-strand	135-138	4	18
β-strand	142	1	19
β-strand	143	1	17
β-strand	147-151	5	20
β-strand	162-164	3	18
β-strand	167	1	19
β-strand	173	1	19
β-strand	176-179	4	18
β-strand	188-194	7	20
β-strand	201-207	7	20
α-helix	224-293	70
β-strand	297-299	3	21
α-helix	300-302	3
β-strand	304	1	22
β-strand	313-314	2	23
β-strand	321-322	2	21
β-strand	323-324	2	23
β-strand	346-348	3	24
β-strand	349	1	22
β-strand	353	1	24
β-strand	357-363	7	21
β-strand	371-376	6	24
β-strand	393-397	5	24
β-strand	398	1	25
β-strand	403	1	25
β-strand	413	1	25
β-strand	421-427	7	21
β-strand	432	1	21
β-strand	435-437	3	21
β-strand	442	1	21
β-strand	445	1	26
α-helix	447-449	3
β-strand	456-461	6	24
β-strand	469-471	3	21
α-helix	472-474	3
β-strand	488-489	2	27

Chain F: 7 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	28
β-strand	11-14	4	29
β-strand	19-25	7	28
β-strand	38	1	30
β-strand	39	1	31
β-strand	48	1	30
α-helix	51-53	3
β-strand	69-71	3	28
β-strand	79-84	6	28
α-helix	89-91	3
β-strand	93-95	3	29
β-strand	96	1	31
β-strand	101	1	32
β-strand	104	1	32
β-strand	110-115	6	29
β-strand	122-124	3	33
β-strand	128	1	33
β-strand	133-138	6	33
β-strand	147-149	3	34
β-strand	177-181	5	33
β-strand	190-195	6	34
β-strand	200-205	6	34
α-helix	224-293	70
β-strand	297	1	35
β-strand	298-299	2	21
β-strand	304	1	36
β-strand	313-315	3	37
β-strand	321-324	4	37
β-strand	346-348	3	38
β-strand	349	1	36
β-strand	353	1	38
β-strand	357-358	2	35
β-strand	361-362	2	27
β-strand	370-376	7	38
β-strand	393-399	7	38
β-strand	402-405	4	38
β-strand	412	1	38
β-strand	422-423	2	27
β-strand	426-427	2	35
β-strand	432	1	35
β-strand	435-437	3	27
β-strand	442-446	5	27
α-helix	447-449	3
β-strand	456-462	7	38
α-helix	468	1
β-strand	469-470	2	37
β-strand	471	1	27
α-helix	472-474	3
α-helix	482-484	3
β-strand	489	1	26

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)
Butyrophilin subfamily 2 member A1	E, F	protein	532	Homo sapiens	Q7KYR7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9JQQ_1 Butyrophilin subfamily 3 member A1 (chains A)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSD
LHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVI
MRGSSGEGVSCTIRSSLLGLEKTASISIADPFFRSAQRWIAALAGTLPVLLLLLGGAGYF
LWQQQEEKKTQFRKKKREQELREMAWSTMKQEQSTRVKLLEELRWRSIQYASRGERHSAY
NEWKKALFKPADVILDPKTANPILLVSEDQRSVQRAKEPQDLPDNPERFNWHYCVLGCES
FISGRHYWEVEVGDRKEWHIGVCSKNVQRKGWVKMTPENGFWTMGLTDGNKYRTLTEPRT
NLKLPKPPKKVGVFLDYETGDISFYNAVDGSHIHTFLDVSFSEALYPVFRILTLEPTALT
ICPAGGGGSGGGGSGGGGSWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Sequence of entity 2 (B), FASTA

>9JQQ_2 Butyrophilin subfamily 3 member A2 (chains B)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSN
LHVEVKGYEDGGIHLECRSTGWYPQPQIQWSNAKGENIPAVEAPVVADGVGLYEVAASVI
MRGGSGEGVSCIIRNSLLGLEKTASISIADPFFRSAQPWIAALAGTLPILLLLLAGASYF
LWRQQKEITALSSEIESEQEMKEMGYAATEREISLRESLQEELKRKKIQYLTRGEESSSD
TNKSAGGGGSDYKDDDDK

Sequence of entity 3 (E, F), FASTA

>9JQQ_3 Butyrophilin subfamily 2 member A1 (chains E, F)
QFIVVGPTDPILATVGENTTLRCHLSPEKNAEDMEVRWFRSQFSPAVFVYKGGRERTEEQ
MEEYRGRTTFVSKDISRGSVALVIHNITAQENGTYRCYFQEGRSYDEAILHLVVAGLGSK
PLISMRGHEDGGIRLECISRGWYPKPLTVWRDPYGGVAPALKEVSMPDADGLFMVTTAVI
IRDKSVRNMSCSINNTLLGQKKESVIFIPESFMPSVSPCAVALPIIVVILMIPIAVCIYW
INKLQKEKKILSGEKEFERETREIALKELEKERVQKEEELQVKEKLQEELRWRRTFLHAV
DVVLDPDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNPERFDSQPCVLGRESFASGKHYW
EVEVENVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEMHKGQYRAVSSPDRILPLKESLC
RVGVFLDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRPFFRLGCEDSPIFICPALTGANG
VTVPEEGLTLHRVGTHQSLGGGGSWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
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

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