8JYC: Intracellular B30.2 Domain of BTN3A1 and BTN2A1

Crystal Structure of Intracellular B30.2 Domain of BTN3A1 and BTN2A1 in Complex with DMAPP. Determined by X-ray diffraction at 2.29 Å resolution. Released 13 Sept 2023.

Method: X-ray diffraction
Resolution: 2.29 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,669
Mol. weight: 97.67 kDa
Ligands: DMA
Released: 13 Sept 2023

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

Secondary structure: helices and β-sheets

8JYC contains 21 α-helices and 70 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: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	325-327	3	1
β-strand	332	1	2
α-helix	334-336	3
β-strand	341-343	3	1
β-strand	349-352	4	1
β-strand	374-376	3	3
β-strand	377	1	2
β-strand	381	1	3
β-strand	385-391	7	1
β-strand	398-404	7	3
α-helix	417-419	3
β-strand	421-427	7	3
β-strand	430-433	4	3
β-strand	440	1	3
β-strand	449-455	7	1
β-strand	460-465	6	1
β-strand	470-474	5	1
α-helix	475-477	3
β-strand	484-490	7	3
α-helix	496	1
β-strand	497-500	4	1
α-helix	501-503	3
β-strand	516-517	2	1

Chain B: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	324	1
β-strand	325-327	3	1
β-strand	332	1	4
α-helix	334-336	3
β-strand	341-343	3	1
β-strand	349-352	4	1
β-strand	374-376	3	5
β-strand	377	1	4
β-strand	381	1	5
β-strand	385-391	7	1
β-strand	398-404	7	5
α-helix	417-419	3
β-strand	421-427	7	5
β-strand	430-433	4	5
β-strand	440-441	2	5
β-strand	449-455	7	1
α-helix	456-458	3
β-strand	460-465	6	1
β-strand	470-474	5	1
α-helix	475-477	3
β-strand	484-490	7	5
β-strand	497-499	3	1
α-helix	500-503	4
β-strand	516-517	2	1

Chain C: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	304-306	3
β-strand	308-309	2	6
β-strand	314	1	7
α-helix	316-318	3
β-strand	323-325	3	6
β-strand	331-334	4	6
β-strand	353-355	3	8
β-strand	356	1	7
α-helix	359	1
β-strand	360	1	8
β-strand	364-370	7	6
β-strand	377-383	7	8
α-helix	396-398	3
β-strand	400-406	7	8
β-strand	410-413	4	8
β-strand	419-420	2	8
α-helix	421-422	2
β-strand	429-435	7	6
β-strand	440-445	6	6
β-strand	451-455	5	6
β-strand	464-469	6	8
α-helix	477	1
β-strand	478-480	3	6
α-helix	481-483	3

Chain D: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	308-309	2	9
α-helix	310	1
β-strand	314	1	10
β-strand	323-325	3	9
β-strand	331-334	4	9
β-strand	353-355	3	11
β-strand	356	1	10
β-strand	360	1	11
β-strand	364-370	7	9
β-strand	377-383	7	11
α-helix	396-398	3
β-strand	400-406	7	11
β-strand	410-413	4	11
β-strand	419-420	2	11
α-helix	426-427	2
β-strand	429-435	7	9
β-strand	440-445	6	9
β-strand	451-455	5	9
β-strand	464-469	6	11
β-strand	478-480	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Butyrophilin subfamily 2 member A1	A, B	protein	218	Homo sapiens	Q7KYR7 (AlphaFold model)
Butyrophilin subfamily 3 member A1	C, D	protein	196	Homo sapiens	O00481 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8JYC_1 Butyrophilin subfamily 2 member A1 (chains A, B)
GAGAGAEELRWRRTFLHAVDVVLDPDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNPERF
DSQPCVLGRESFASGKHYWEVEVENVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEMHKG
QYRAVSSPDRILPLKESLCRVGVFLDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRPFFR
LGCEDSPIFICPALTGANGVTVPEEGLTLHRVGTHQSL

Sequence of entity 2 (C, D), FASTA

>8JYC_2 Butyrophilin subfamily 3 member A1 (chains C, D)
MGAYNEWKKALFKPADVILDPKTANPILLVSEDQRSVQRAKEPQDLPDNPERFNWHYCVL
GCESFISGRHYWEVEVGDRKEWHIGVCSKNVQRKGWVKMTPENGFWTMGLTDGNKYRTLT
EPRTNLKLPKPPKKVGVFLDYETGDISFYNAVDGSHIHTFLDVSFSEALYPVFRILTLEP
TALTICPALEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
DMA	Dimethylallyl diphosphate	C5 H12 O7 P2	2

Water and common crystallization additives (EDO, 1PE, PG4, PGE, PEG) are not listed.

Primary citation

Phosphoantigens glue butyrophilin 3A1 and 2A1 to activate V gamma 9V delta 2 T cells. Yuan, L., Ma, X., Yang, Y. et al. Nature (2023) 621:840-848. DOI 10.1038/s41586-023-06525-3 · 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
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…
8ZJX 3.35 Å, Cryo-EM structure of the full length pAg-bound BTN2A1-BTN3A1-BTN3A2 in complex with…

Browse structure collections

About this viewer

MolViewer shows 8JYC directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.