8ZA6: GdTCR-CD3 complex

Cryo-EM structure of the gdTCR-CD3 complex. Determined by electron microscopy at 3.43 Å resolution. Released 30 Apr 2025.

Method: Electron microscopy
Resolution: 3.43 Å
Organism: Homo sapiens
Chains: 8
Atoms: 4,669
Mol. weight: 193.51 kDa
Ligands: CLR
Released: 30 Apr 2025

Explore 8ZA6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZA6 contains 14 α-helices and 38 β-strands across 8 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	33-53	21

Chain b: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	30-52	23

Chain d: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	27-28	2	1
β-strand	33-35	3	1
α-helix	40-41	2
β-strand	43-46	4	2
β-strand	50-51	2	1
β-strand	58-59	2	1
α-helix	63-65	3
β-strand	68-73	6	2
β-strand	84-91	8	2
β-strand	96-98	3	3
α-helix	101-126	26

Chain e: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37-41	5	4
β-strand	44-48	5	4
β-strand	57-61	5	2
β-strand	65-66	2	2
β-strand	75-77	3	4
β-strand	82-85	4	4
β-strand	95-100	6	2
β-strand	101	1	5
β-strand	103	1	5
α-helix	105-107	3
β-strand	111-116	6	2
β-strand	122-124	3	3
α-helix	127-151	25
α-helix	152-154	3

Chain f: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	37-41	5	6
β-strand	44-48	5	6
β-strand	58-59	2	7
β-strand	60	1	8
β-strand	65	1	8
β-strand	81-84	4	6
β-strand	94-96	3	9
β-strand	98-99	2	7
β-strand	111-116	6	9
β-strand	122-124	3	10
α-helix	127-155	29

Chain g: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	11
β-strand	41-46	6	11
β-strand	54-56	3	12
β-strand	61-64	4	12
β-strand	71-76	6	11
α-helix	77-79	3
β-strand	82-85	4	9
β-strand	87	1	12
β-strand	97-102	6	9
β-strand	107-109	3	10
α-helix	114-137	24

Chain m: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	259-288	30

Chain n: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	284-319	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD3 zeta chain	a, b	protein	165	Homo sapiens	P20963 (AlphaFold model)
T-cell surface glycoprotein CD3 delta chain	d	protein	171	Homo sapiens	P04234 (AlphaFold model)
T-cell surface glycoprotein CD3 epsilon chain	e, f	protein	207	Homo sapiens	P07766 (AlphaFold model)
T-cell surface glycoprotein CD3 gamma chain	g	protein	182	Homo sapiens	P09693 (AlphaFold model)
TRA@ protein	m	protein	290	Homo sapiens	Q6PJ56
CD3	n	protein	328	Homo sapiens

Sequence of entity 1 (a, b), FASTA

>8ZA6_1 T-cell surface glycoprotein CD3 zeta chain (chains a, b)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRS

Sequence of entity 2 (d), FASTA

>8ZA6_2 T-cell surface glycoprotein CD3 delta chain (chains d)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Sequence of entity 3 (e, f), FASTA

>8ZA6_3 T-cell surface glycoprotein CD3 epsilon chain (chains e, f)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 4 (g), FASTA

>8ZA6_4 T-cell surface glycoprotein CD3 gamma chain (chains g)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RN

Sequence of entity 5 (m), FASTA

>8ZA6_5 TRA@ protein (chains m)
MLFSSLLCVFVAFSYSGSSVAQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQL
PSKEMIFLIRQGSDEQNAKSGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGDPGGLN
TDKLIFGKGTRVTVEPRSQPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEF
DPAIVISPSGKYNAVKLGKYEDSNSVTCSVQHDNKTVHSTDFEVKTDSTDHVKPKETENT
KQPSKSCHKPKAIVHTEKVNMMSLTVLGLRMLFAKTVAVNFLLTAKLFFL

Sequence of entity 6 (n), FASTA

>8ZA6_6 CD3 (chains n)
MRVALVVLLAFLSPASQKSSNLEGGTKSVTRPTRSSAEITCDLTVINAFYIHWYLHQEGK
APQRLLYYDVSNSKDVLESGLSPGKYYTHTPRRWSWILILRNLIENDSGVYYCATWDRGN
PKTHYYKKLFGSGTTLVVTDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDV
IKIHWQEKKSNTILGSQEGNTMKTNDTYMKFSWLTVPEESLDKEHRCIVRHENNKNGVDG
EIIFPPIKTDVITMDPKDNASKDANDVITMDPKDNWSKDANDTLLLQLTNTSAYYTYLLL
LLKSVVYFAIITCCLLRRTAFCCNGEKS

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	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 P20963 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2OQ1 1.9 Å, Tandem SH2 domains of ZAP-70 with 19-mer zeta1 peptide
3IK5 2.05 Å, SIVmac239 Nef in complex with TCR zeta ITAM 1 polypeptide (A63-R80)
8ES8 2.65 Å, CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239)
4XZ1 2.8 Å, ZAP-70-tSH2:Compound-B adduct
1YGR 2.9 Å, Crystal structure of the tandem phosphatase domain of RPTP CD45
7FJE 3.0 Å, Cryo-EM structure of a membrane protein(LL)
9CI8 3.01 Å, T cell receptor complex
8ES7 3.04 Å, CryoEM structure of PN45545 TCR-CD3 complex
7PHR 3.08 Å, Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I
9JY1 3.08 Å, delta epsilon/delta epsilon Fab-TCR tetramer
7FJF 3.1 Å, Cryo-EM structure of a membrane protein(CS)
8TW6 3.1 Å, TCR in nanodisc ND-II

Browse structure collections

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