8ZD4: GdTCR-ECD

Cryo-EM structure of the gdTCR-ECD. Determined by electron microscopy at 2.9 Å resolution. Released 7 May 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,795
Mol. weight: 97.08 kDa
Released: 7 May 2025

Explore 8ZD4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZD4 contains 22 α-helices and 89 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: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	23-25	3	1
β-strand	31-34	4	2
β-strand	41-46	6	1
β-strand	53-60	8	3
β-strand	64-70	7	3
β-strand	78-80	3	1
β-strand	83-88	6	1
β-strand	93-98	6	1
α-helix	103-105	3
β-strand	108	1	3
β-strand	111-115	5	3
β-strand	123-126	4	3
β-strand	132-135	4	2
β-strand	142	1	4
β-strand	146-150	5	5
β-strand	154	1	6
β-strand	155-162	8	5
β-strand	163	1	4
β-strand	168-172	5	7
β-strand	176-179	4	6
α-helix	185	1
β-strand	186	1	5
α-helix	187	1
β-strand	192-196	5	5
β-strand	198-200	3	6
β-strand	207-212	6	7
β-strand	215-217	3	7
α-helix	220-222	3

Chain B: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	27-31	5	8
β-strand	37-41	5	9
β-strand	50-53	4	10
β-strand	56	1	8
β-strand	62	1	8
β-strand	66-69	4	10
β-strand	74-77	4	10
α-helix	78	1
α-helix	81-82	2
β-strand	86-89	4	9
β-strand	96-100	5	9
α-helix	105-107	3
β-strand	109-110	2	8
β-strand	113-117	5	10
β-strand	127-130	4	10
β-strand	134-138	5	8
β-strand	150-154	5	11
α-helix	155-157	3
α-helix	160-164	5
β-strand	167-176	10	11
β-strand	183-186	4	12
α-helix	193-195	3
β-strand	197-198	2	11
β-strand	202-203	2	11
β-strand	208-216	9	11
α-helix	218-220	3
β-strand	225-229	5	12
α-helix	235-237	3
β-strand	240-244	5	12
α-helix	245-247	3

Chain D: 3 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	23-25	3	13
β-strand	30-34	5	14
β-strand	39-46	8	13
β-strand	53-59	7	14
β-strand	65	1	14
β-strand	69-70	2	14
β-strand	79-80	2	13
β-strand	83-88	6	13
β-strand	93-98	6	13
β-strand	108-115	8	14
β-strand	123-126	4	14
β-strand	130-135	6	14
α-helix	136-138	3
β-strand	142	1	15
β-strand	146-150	5	16
β-strand	154	1	17
β-strand	155-162	8	16
β-strand	163	1	15
β-strand	168-172	5	18
β-strand	178-179	2	17
β-strand	185	1	19
β-strand	192	1	16
β-strand	193	1	19
β-strand	194-196	3	16
β-strand	198-199	2	17
α-helix	203-205	3
β-strand	207-212	6	18
β-strand	215-217	3	18
α-helix	220-222	3

Chain G: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	27-32	6	20
β-strand	37-40	4	21
β-strand	50-56	7	20
β-strand	62-69	8	20
β-strand	74-76	3	20
α-helix	81-82	2
β-strand	86-92	7	21
β-strand	95-100	6	21
α-helix	105-107	3
β-strand	109-117	9	20
β-strand	127-130	4	20
β-strand	134-139	6	20
β-strand	150-154	5	22
α-helix	155-157	3
α-helix	158-164	7
β-strand	166-174	9	22
β-strand	182-186	5	23
β-strand	197-198	2	22
β-strand	202-203	2	22
β-strand	208-217	10	22
α-helix	218-220	3
β-strand	225-230	6	23
α-helix	235-237	3
β-strand	240-244	5	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TRA@ protein	A, D	protein	202	Homo sapiens	Q6PJ56 (AlphaFold model)
gamma chain	B, G	protein	224	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>8ZD4_1 TRA@ protein (chains A, D)
QKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKSG
RYSVNFKKAAKSVALTISALQLEDSAKYFCALGDPGGLNTDKLIFGKGTRVTVEPRSQPH
TKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLGKYE
DSNSVTCSVQHDNKTVHSTDFE

Sequence of entity 2 (B, G), FASTA

>8ZD4_2 gamma chain (chains B, G)
GTKSVTRPTRSSAEITCDLTVINAFYIHWYLHQEGKAPQRLLYYDVSNSKDVLESGLSPG
KYYTHTPRRWSWILILRNLIENDSGVYYCATWDRGNPKTHYYKKLFGSGTTLVVTDKQLD
ADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILGSQEGNTMKT
NDTYMKFSWLTVPEESLDKEHRCIVRHENNKNGVDQEIIFPPIK

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 Q6PJ56 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LFH 2.3 Å, Crystal Structure of 9C2 TCR
6D7G 2.75 Å, Structure of 5F3 TCR in complex with HLA-A2/MART-1
4LHU 2.87 Å, Crystal Structure of 9C2 TCR bound to CD1d
4MNG 3.01 Å, Structure of the DP10.7 TCR with CD1d-sulfatide
4NDM 3.01 Å, Structure of the AB18.1 TCR
9LSY 3.23 Å, Structure of the gdTCR-Fab complex
4MNH 3.3 Å, Structure of the DP10.7 TCR
8ZA6 3.43 Å, Cryo-EM structure of the gdTCR-CD3 complex

Browse structure collections

About this viewer

MolViewer shows 8ZD4 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.