8ZAA: Intracellular HBMBPP-BTN2A1-BTN3A1 complex

Cryo-EM structure of intracellular HBMBPP-BTN2A1-BTN3A1 complex. Determined by electron microscopy at 3.46 Å resolution. Released 30 Apr 2025.

Method: Electron microscopy
Resolution: 3.46 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,773
Mol. weight: 113.64 kDa
Ligands: EIP
Released: 30 Apr 2025

Explore 8ZAA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZAA contains 18 α-helices and 69 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 C: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	260-289	30
α-helix	299-303	5
β-strand	315	1	1
α-helix	317-319	3
β-strand	324-326	3	2
β-strand	332-335	4	2
α-helix	339-341	3
β-strand	354-356	3	3
β-strand	357	1	1
β-strand	361	1	4
β-strand	365-371	7	2
β-strand	378-383	6	3
α-helix	397-399	3
β-strand	401-407	7	3
β-strand	411-414	4	3
β-strand	420-421	2	3
β-strand	430-436	7	2
β-strand	441-446	6	2
β-strand	452-456	5	2
β-strand	465	1	4
β-strand	466-470	5	3
β-strand	479-482	4	2

Chain D: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	267-291	25
α-helix	300-303	4
β-strand	309-310	2	5
β-strand	315	1	6
β-strand	324-326	3	7
β-strand	333-335	3	7
β-strand	354-356	3	8
β-strand	357	1	6
β-strand	361	1	8
β-strand	365-371	7	5
β-strand	378-384	7	8
β-strand	402-407	6	8
β-strand	411-414	4	8
β-strand	420-421	2	8
β-strand	430-436	7	5
β-strand	441-446	6	5
β-strand	451-456	6	5
β-strand	465-470	6	8
β-strand	480-481	2	5

Chain E: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	241-291	51
β-strand	297-299	3	9
β-strand	304	1	12
α-helix	306-308	3
β-strand	313-315	3	9
β-strand	321-324	4	9
β-strand	346-348	3	13
β-strand	349	1	12
β-strand	353	1	13
β-strand	357-363	7	9
β-strand	370-376	7	13
β-strand	393-399	7	13
β-strand	402-404	3	13
β-strand	421-427	7	9
β-strand	432-437	6	9
β-strand	442-447	6	9
α-helix	448-449	2
β-strand	456-462	7	13
α-helix	468	1
β-strand	469-471	3	9
α-helix	472-474	3
β-strand	488-489	2	9

Chain G: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	241-251	11
α-helix	252-254	3
α-helix	255-292	38
β-strand	297-299	3	9
β-strand	304	1	10
β-strand	313-315	3	9
β-strand	321-324	4	9
β-strand	346-348	3	11
β-strand	349	1	10
β-strand	353	1	11
β-strand	357-363	7	9
β-strand	370-376	7	11
β-strand	393-399	7	11
β-strand	402-404	3	11
β-strand	412	1	11
β-strand	421-427	7	9
α-helix	428-430	3
β-strand	432-437	6	9
β-strand	442-446	5	9
α-helix	447-449	3
β-strand	456-462	7	11
β-strand	469-471	3	9
α-helix	472-474	3
β-strand	489	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Butyrophilin subfamily 3 member A1	C, D	protein	227	Homo sapiens	O00481 (AlphaFold model)
Butyrophilin subfamily 2 member A1	E, G	protein	260	Homo sapiens	Q7KYR7 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>8ZAA_1 Butyrophilin subfamily 3 member A1 (chains C, D)
EQELREMAWSTMKQEQSTRVKLLEELRWRSIQYASRGERHSAYNEWKKALFKPADVILDP
KTANPILLVSEDQRSVQRAKEPQDLPDNPERFNWHYCVLGCESFISGRHYWEVEVGDRKE
WHIGVCSKNVQRKGWVKMTPENGFWTMGLTDGNKYRTLTEPRTNLKLPKTPKKVGVFLDY
ETGDISFYNAVDGSHIHTFLDVSFSEALYPVFRILTLEPTALTICPA

Sequence of entity 2 (E, G), FASTA

>8ZAA_2 Butyrophilin subfamily 2 member A1 (chains E, G)
WINKLQKEKKILSGEKEFERETREIALKELEKERVQKEEELQVKEKLQEELRWRRTFLHA
VDVVLDPDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNPERFDSQPCVLGRESFASGKHY
WEVEVENVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEMHKGQYRAVSSPDRILPLKESL
CRVGVFLDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRPFFRLGCEDSPIFICPALTGAN
GVTVPEEGLTLHRVGTHQSL

Ligands and cofactors

ID	Name	Formula	Copies
EIP	4-hydroxy-3-methyl butyl diphosphate	C5 H14 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 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

Browse structure collections

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