9JQ6: BTN2A1

Cryo-EM structure of BTN2A1 in complex with antagonist antibody TH002. 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: 6
Atoms: 10,236
Mol. weight: 220.4 kDa
Ligands: NAG
Released: 18 Jun 2025

Explore 9JQ6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JQ6 contains 32 α-helices and 138 β-strands across 6 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 E: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
α-helix	10	1
β-strand	11-14	4	2
β-strand	19-23	5	3
β-strand	24-25	2	1
β-strand	35-39	5	2
β-strand	46	1	4
β-strand	48-51	4	2
α-helix	57-59	3
β-strand	60	1	4
β-strand	68-71	4	3
α-helix	75-77	3
β-strand	80-84	5	3
α-helix	89-91	3
β-strand	93-100	8	2
β-strand	105-115	11	2
β-strand	116	1	5
α-helix	119-121	3
β-strand	122-128	7	6
β-strand	133-142	10	6
β-strand	143	1	5
β-strand	147-151	5	7
β-strand	157-158	2	7
α-helix	159-160	2
β-strand	162-163	2	6
β-strand	166-167	2	6
β-strand	173-181	9	6
β-strand	188-195	8	7
β-strand	200-207	8	7
α-helix	210-212	3

Chain F: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
α-helix	10	1
β-strand	11-14	4	9
β-strand	19-23	5	10
β-strand	24-25	2	8
β-strand	35-37	3	9
β-strand	46	1	11
β-strand	51	1	12
β-strand	54	1	12
β-strand	60	1	11
β-strand	68-71	4	10
β-strand	80-84	5	10
α-helix	89-91	3
β-strand	93-101	9	9
β-strand	104-115	12	9
β-strand	116	1	13
α-helix	119-121	3
β-strand	122-129	8	14
β-strand	132-142	11	14
β-strand	143	1	13
β-strand	147-150	4	15
β-strand	158	1	15
β-strand	162-163	2	14
β-strand	166-167	2	14
β-strand	173-181	9	14
β-strand	188-190	3	16
β-strand	191-195	5	15
β-strand	200-202	3	15
β-strand	205-207	3	16
α-helix	210-212	3

Chain H: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	17
β-strand	11-12	2	18
β-strand	17-25	9	17
α-helix	29-31	3
β-strand	33-39	7	19
β-strand	45-51	7	19
β-strand	58-60	3	19
α-helix	63-66	4
β-strand	68-73	6	17
β-strand	78-84	7	17
β-strand	92-100	9	19
β-strand	107-111	5	19
β-strand	115-117	3	19
β-strand	118-119	2	18
β-strand	128-131	4	20
α-helix	133-135	3
β-strand	143-145	3	21
β-strand	148-151	4	20
β-strand	159-162	4	22
β-strand	173-178	6	20
β-strand	183-187	5	20
β-strand	190-192	3	21
α-helix	195-198	4
β-strand	202-206	5	22
β-strand	214-217	4	22
α-helix	218-219	2

Chain I: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	23
β-strand	10-14	5	24
β-strand	19-24	6	23
β-strand	37-42	6	24
β-strand	49-52	4	24
β-strand	58	1	24
α-helix	59	1
β-strand	66-67	2	23
β-strand	76-79	4	23
α-helix	84-86	3
β-strand	89-94	6	24
α-helix	100-101	2
β-strand	102	1	24
β-strand	106-111	6	24
β-strand	115	1	25
α-helix	116-117	2
β-strand	118-122	5	26
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-134	2	27
β-strand	137-143	7	26
β-strand	144	1	25
β-strand	148-153	6	28
β-strand	157	1	28
β-strand	163-167	5	26
α-helix	169-171	3
β-strand	177-183	7	26
β-strand	185-186	2	27
α-helix	187-192	6
β-strand	196-202	7	28
β-strand	205-213	9	28

Chain J: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	29
β-strand	10-12	3	30
β-strand	17-25	9	29
α-helix	29-31	3
β-strand	33-39	7	30
β-strand	45-51	7	30
β-strand	58-60	3	30
α-helix	62-64	3
β-strand	68-73	6	29
β-strand	78-84	7	29
β-strand	92-100	9	30
β-strand	107-111	5	30
β-strand	115-119	5	30
β-strand	129-130	2	31
α-helix	136-138	3
β-strand	143-146	4	31
β-strand	149-151	3	31
β-strand	159-162	4	32
α-helix	163-165	3
β-strand	171-179	9	31
β-strand	182-192	11	31
β-strand	201-202	2	33
β-strand	203-207	5	32
β-strand	212-214	3	32
β-strand	217-218	2	33

Chain K: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	34
β-strand	11-14	4	35
β-strand	19-25	7	34
β-strand	30-31	2	36
β-strand	34-35	2	36
β-strand	39-42	4	37
β-strand	49-52	4	37
β-strand	58	1	37
β-strand	66-71	6	34
β-strand	74-79	6	34
α-helix	84-86	3
β-strand	89-91	3	37
β-strand	93	1	38
α-helix	100	1
β-strand	102	1	38
β-strand	106-107	2	37
β-strand	108-111	4	35
β-strand	115	1	39
β-strand	118-122	5	40
α-helix	123-125	3
α-helix	126-131	6
β-strand	137-143	7	40
β-strand	144	1	39
β-strand	151-153	3	41
β-strand	166-167	2	40
β-strand	177-182	6	40
β-strand	196-200	5	41
β-strand	209-213	5	41

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Butyrophilin subfamily 2 member A1	E, F	protein	532	Homo sapiens	Q7KYR7 (AlphaFold model)
BTN2A1 antagonist antibody TH002-Fab heavy chain	H, J	protein	231	Mus musculus
BTN2A1 antagonist antibody TH002-Fab light chain	I, K	protein	218	Mus musculus

Sequence of entity 1 (E, F), FASTA

>9JQ6_1 Butyrophilin subfamily 2 member A1 (chains E, F)
QFIVVGPTDPILATVGENTTLRCHLSPEKNAEDMEVRWFRSQFSPAVFVYKGGRERTEEQ
MEEYRGRTTFVSKDISRGSVALVIHNITAQENGTYRCYFQEGRSYDEAILHLVVAGLGSK
PLISMRGHEDGGIRLECISRGWYPKPLTVWRDPYGGVAPALKEVSMPDADGLFMVTTAVI
IRDKSVRNMSCSINNTLLGQKKESVIFIPESFMPSVSPCAVALPIIVVILMIPIAVCIYW
INKLQKEKKILSGEKEFERETREIALKELEKERVQKEEELQVKEKLQEELRWRRTFLHAV
DVVLDPDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNPERFDSQPCVLGRESFASGKHYW
EVEVENVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEMHKGQYRAVSSPDRILPLKESLC
RVGVFLDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRPFFRLGCEDSPIFICPALTGANG
VTVPEEGLTLHRVGTHQSLGGGGSWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Sequence of entity 2 (H, J), FASTA

>9JQ6_2 BTN2A1 antagonist antibody TH002-Fab heavy chain (chains H, J)
EVKLLESGGGLVQPGGSLKLSCAASGFDFSRYWMSWVRQAPGKGLEWIGEINPGSITINY
TPSLKDKFIISRDNAKNTLYLQMSKVSSEDTALYYCARQRKWFRRDAMDYWGQGTSVTVS
SAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQS
DLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTIKPCPPC

Sequence of entity 3 (I, K), FASTA

>9JQ6_3 BTN2A1 antagonist antibody TH002-Fab light chain (chains I, K)
DIVLTQSPASLAVSLGQRATVSCKASHSVDYDGDSYVNWYQQKPGQPPKLLISAASNLES
GIPARFSGSGSGTDFTLNIHPVEEEDAATYYCQQSYGDPWTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

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 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
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…

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