9JQP: HMBPP-primed BTN3A1-BTN3A2-BTN2A1

Cryo-EM structure of the HMBPP-primed BTN3A1-BTN3A2-BTN2A1 in complex with agonist antibody TH001. Determined by electron microscopy at 3.34 Å resolution. Released 18 Jun 2025.

Method: Electron microscopy
Resolution: 3.34 Å
Organisms: Homo sapiens, Mus musculus
Chains: 7
Atoms: 8,175
Mol. weight: 204.37 kDa
Ligands: NAG
Released: 18 Jun 2025

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

Secondary structure: helices and β-sheets

9JQP contains 12 α-helices and 118 β-strands across 7 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, 24 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	1
β-strand	20-21	2	2
β-strand	38-40	3	3
β-strand	46	1	3
β-strand	49	1	4
β-strand	56	1	4
α-helix	62-64	3
β-strand	68-70	3	2
β-strand	82-84	3	2
α-helix	89-91	3
β-strand	93-94	2	1
β-strand	95-97	3	3
β-strand	99-100	2	5
β-strand	105-106	2	5
β-strand	111-115	5	1
β-strand	116	1	6
β-strand	122-129	8	7
β-strand	132-138	7	7
β-strand	142	1	8
β-strand	143	1	6
α-helix	145-146	2
β-strand	147-151	5	9
α-helix	163-165	3
β-strand	173	1	8
β-strand	176	1	7
β-strand	179-180	2	7
β-strand	189-194	6	9
β-strand	201-207	7	9

Chain B: 2 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	10
β-strand	11-14	4	11
β-strand	19-26	8	10
β-strand	35-37	3	11
β-strand	40	1	11
β-strand	49	1	11
β-strand	56	1	11
β-strand	68-70	3	10
α-helix	72-74	3
β-strand	79-84	6	10
β-strand	93-100	8	11
β-strand	101	1	12
β-strand	104	1	12
β-strand	107-115	9	11
β-strand	116	1	13
α-helix	119-121	3
β-strand	122-125	4	9
β-strand	133-142	10	9
β-strand	143	1	13
β-strand	147-151	5	14
β-strand	166	1	9
β-strand	173-176	4	9
β-strand	179-181	3	9
β-strand	189	1	7
β-strand	190-195	6	14
β-strand	200-203	4	14
β-strand	206	1	7

Chain E: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	15
β-strand	11-14	4	16
β-strand	19-23	5	17
β-strand	24-25	2	15
β-strand	35-39	5	16
β-strand	48-51	4	16
β-strand	54-55	2	16
α-helix	62-64	3
β-strand	69-71	3	17
β-strand	80-84	5	17
β-strand	93-98	6	16
β-strand	101	1	18
β-strand	104	1	18
β-strand	109-115	7	16
β-strand	116	1	19
α-helix	119-121	3
β-strand	122-125	4	20
β-strand	135-140	6	20
β-strand	143	1	19
β-strand	150	1	21
β-strand	174-179	6	20
β-strand	188-194	7	21
β-strand	201-207	7	21

Chain H: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	22
β-strand	19-20	2	23
β-strand	22-23	2	22
α-helix	29-31	3
β-strand	33-34	2	24
β-strand	36-40	5	25
β-strand	43-51	9	25
β-strand	58-60	3	25
β-strand	65	1	26
β-strand	68	1	26
β-strand	69-70	2	23
α-helix	74-76	3
β-strand	81-82	2	23
β-strand	93-95	3	25
β-strand	98-99	2	24
β-strand	110-112	3	25

Chain I: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	27
β-strand	10	1	28
β-strand	22-25	4	27
β-strand	30	1	29
β-strand	36	1	29
β-strand	39-42	4	30
β-strand	50-54	5	30
β-strand	75-77	3	27
β-strand	91-94	4	30
β-strand	104	1	27
β-strand	108	1	28

Chain J: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	31
β-strand	10	1	32
β-strand	18-23	6	31
α-helix	29-31	3
β-strand	33-39	7	33
β-strand	45-51	7	33
β-strand	58-60	3	33
β-strand	68-73	6	31
β-strand	78-83	6	31
β-strand	93-99	7	33
β-strand	107	1	33
β-strand	113	1	32

Chain K: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	34
β-strand	10-12	3	35
β-strand	18-25	8	34
β-strand	38-39	2	33
β-strand	40-43	4	36
β-strand	50-53	4	36
β-strand	67-72	6	34
β-strand	75-81	7	34
β-strand	90-91	2	36
β-strand	94-95	2	33
α-helix	101	1
β-strand	102	1	33
β-strand	108-110	3	35

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	protein	532	Homo sapiens	Q7KYR7 (AlphaFold model)
BTN3A agonist antibody TH001, variable domain of heavy chain	H, J	protein	117	Mus musculus
BTN3A agonist antibody TH001, variable domain of light chain	I, K	protein	112	Mus musculus

Sequence of entity 1 (A), FASTA

>9JQP_1 Butyrophilin subfamily 3 member A1 (chains A)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSD
LHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVI
MRGSSGEGVSCTIRSSLLGLEKTASISIADPFFRSAQRWIAALAGTLPVLLLLLGGAGYF
LWQQQEEKKTQFRKKKREQELREMAWSTMKQEQSTRVKLLEELRWRSIQYASRGERHSAY
NEWKKALFKPADVILDPKTANPILLVSEDQRSVQRAKEPQDLPDNPERFNWHYCVLGCES
FISGRHYWEVEVGDRKEWHIGVCSKNVQRKGWVKMTPENGFWTMGLTDGNKYRTLTEPRT
NLKLPKPPKKVGVFLDYETGDISFYNAVDGSHIHTFLDVSFSEALYPVFRILTLEPTALT
ICPAGGGGSGGGGSGGGGSWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Sequence of entity 2 (B), FASTA

>9JQP_2 Butyrophilin subfamily 3 member A2 (chains B)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSN
LHVEVKGYEDGGIHLECRSTGWYPQPQIQWSNAKGENIPAVEAPVVADGVGLYEVAASVI
MRGGSGEGVSCIIRNSLLGLEKTASISIADPFFRSAQPWIAALAGTLPILLLLLAGASYF
LWRQQKEITALSSEIESEQEMKEMGYAATEREISLRESLQEELKRKKIQYLTRGEESSSD
TNKSAGGGGSDYKDDDDK

Sequence of entity 3 (E), FASTA

>9JQP_3 Butyrophilin subfamily 2 member A1 (chains E)
QFIVVGPTDPILATVGENTTLRCHLSPEKNAEDMEVRWFRSQFSPAVFVYKGGRERTEEQ
MEEYRGRTTFVSKDISRGSVALVIHNITAQENGTYRCYFQEGRSYDEAILHLVVAGLGSK
PLISMRGHEDGGIRLECISRGWYPKPLTVWRDPYGGVAPALKEVSMPDADGLFMVTTAVI
IRDKSVRNMSCSINNTLLGQKKESVIFIPESFMPSVSPCAVALPIIVVILMIPIAVCIYW
INKLQKEKKILSGEKEFERETREIALKELEKERVQKEEELQVKEKLQEELRWRRTFLHAV
DVVLDPDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNPERFDSQPCVLGRESFASGKHYW
EVEVENVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEMHKGQYRAVSSPDRILPLKESLC
RVGVFLDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRPFFRLGCEDSPIFICPALTGANG
VTVPEEGLTLHRVGTHQSLGGGGSWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Sequence of entity 4 (H, J), FASTA

>9JQP_4 BTN3A agonist antibody TH001, variable domain of heavy chain (chains H, J)
EVHVKQSGAELARPGTSVKLSCKASGYTFTDYYLNWVKQRTGQGLEWIGEIYPGGGNTYY
NEKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCARRTTVVGDYWGQGTTLTVSS

Sequence of entity 5 (I, K), FASTA

>9JQP_5 BTN3A agonist antibody TH001, variable domain of light chain (chains I, K)
DVLMTQTPLSLPVSLGDQASISCRSSQSIVNSKGNTYLEWYVQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPWTFGGGTKLEIK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

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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