9L1P: Butyrophilin subfamily 2 member A1

Cryo-EM structure of the ICT01-BTN2A1/BTN3A1/BTN3A2 complex, local refinement. Determined by electron microscopy at 3.5 Å resolution. Released 17 Dec 2025.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,173
Mol. weight: 151.62 kDa
Released: 17 Dec 2025

Explore 9L1P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L1P contains 13 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 B: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	1
α-helix	38	1
β-strand	39-42	4	2
β-strand	47-53	7	1
β-strand	63-67	5	2
β-strand	76-78	3	2
β-strand	83	1	2
β-strand	96-99	4	1
β-strand	107-112	6	1
β-strand	121-129	9	2
β-strand	132-143	12	2

Chain E: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	33-34	2	3
β-strand	40-42	3	4
β-strand	50-54	5	3
β-strand	64-69	6	4
β-strand	75-80	6	4
β-strand	83-84	2	4
α-helix	91-93	3
β-strand	97-100	4	3
β-strand	108-113	6	3
α-helix	118-120	3
β-strand	122-129	8	4
β-strand	134-143	10	4

Chain H: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
α-helix	7-9	3
β-strand	10-12	3	6
β-strand	16-25	10	5
α-helix	29-31	3
β-strand	34-39	6	6
β-strand	45-51	7	6
β-strand	58-60	3	6
β-strand	68-73	6	5
β-strand	78-86	9	5
α-helix	88-90	3
β-strand	92-99	8	6
β-strand	109-112	4	6
β-strand	116-120	5	6
β-strand	126	1	7
β-strand	129-132	4	8
α-helix	133-136	4
β-strand	144-154	11	8
β-strand	155	1	7
β-strand	161-163	3	9
α-helix	164-166	3
β-strand	168	1	9
β-strand	178-179	2	8
β-strand	185-194	10	8
β-strand	203-204	2	10
β-strand	205-207	3	9
β-strand	216	1	9
β-strand	219-220	2	10

Chain L: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-12	3	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-65	4	11
β-strand	72-75	4	11
β-strand	85-90	6	12
α-helix	96	1
β-strand	97-98	2	12
β-strand	102-105	4	12
β-strand	111	1	13
α-helix	112-113	2
β-strand	114-118	5	14
α-helix	123-126	4
β-strand	130-137	8	14
β-strand	139	1	15
β-strand	140	1	13
β-strand	146-150	5	16
β-strand	154	1	16
β-strand	160-163	4	14
β-strand	173	1	15
β-strand	175-181	7	14
α-helix	183-185	3
β-strand	192-196	5	16
β-strand	205	1	16
β-strand	208-209	2	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Butyrophilin subfamily 2 member A1	B	protein	534	Homo sapiens	Q7KYR7 (AlphaFold model)
Butyrophilin subfamily 3 member A2	E	protein	340	Homo sapiens	P78410 (AlphaFold model)
ICT01 heavy chain	H	protein	255	Homo sapiens
ICT01 light chain	L	protein	236	Homo sapiens

Sequence of entity 1 (B), FASTA

>9L1P_1 Butyrophilin subfamily 2 member A1 (chains B)
MDMRVPAQLLGLLLLWLSGARCQFIVVGPTDPILATVGENTTLRCHLSPEKNAEDMEVRW
FRSQFSPAVFVYKGGRERTEEQMEEYRGRTTFVSKDISRGSVALVIHNITAQENGTYRCY
FQEGRSYDEAILHLVVAGLGSKPLISMRGHEDGGIRLECISRGWYPKPLTVWRDPYGGVA
PALKEVSMPDADGLFMVTTAVIIRDKSVRNMSCSINNTLLGQKKESVIFIPESFMPSVSP
CAVALPIIVVILMIPIAVCIYWINKLQKEKKILSGEKEFERETREIALKELEKERVQKEE
ELQVKEKLQEELRWRRTFLHAVDVVLDPDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNP
ERFDSQPCVLGRESFASGKHYWEVEVENVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEM
HKGQYRAVSSPDRILPLKESLCRVGVFLDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRP
FFRLGCEDSPIFICPALTGANGVTVPEEGLTLHRVGTHQSLGSSGMDYKDDDDK

Sequence of entity 2 (E), FASTA

>9L1P_2 Butyrophilin subfamily 3 member A2 (chains E)
MDMRVPAQLLGLLLLWLSGARCQFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKW
VSSSLRQVVNVYADGKEVEDRQSAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCY
FQDGDFYEKALVELKVAALGSNLHVEVKGYEDGGIHLECRSTGWYPQPQIQWSNAKGENI
PAVEAPVVADGVGLYEVAASVIMRGGSGEGVSCIIRNSLLGLEKTASISIADPFFRSAQP
WIAALAGTLPILLLLLAGASYFLWRQQKEITALSSEIESEQEMKEMGYAATEREISLRES
LQEELKRKKIQYLTRGEESSSDTNKSAGSSGMDYKDDDDK

Sequence of entity 3 (H), FASTA

>9L1P_3 ICT01 heavy chain (chains H)
MEFGLSWLFLVAILKGVQCQVQLVQSGAEVKKPGASVKLSCKASGYIFTRYYMYWVKQRP
GQGLEWIGEINPNNGGTKFNEKFKNRATLTVDKSISTAYMELSRLRSDDTAVYYCSREDD
YDGTPFAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTV
SWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVE
PKSCGGSHHHHHHHH

Sequence of entity 4 (L), FASTA

>9L1P_4 ICT01 light chain (chains L)
MDMRVPAQLLGLLLLWLSGARCDIQMTQSPSSLSASVGDRVTITCHASQNINVWLSWYQQ
KPGKAPKLLIYKASNLHTGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQGQTYPYTF
GQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN
SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Local refinement of the ICT01-BTN2A1/BTN3A1/BTN3A2 complex at 3.7 Angstroms reolution. Xin, W.Z., Huang, B.D., Zhou, Q. To be published.

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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