9JY1: Delta epsilon/delta epsilon Fab-TCR tetramer

delta epsilon/delta epsilon Fab-TCR tetramer. Determined by electron microscopy at 3.08 Å resolution. Released 22 Oct 2025.

Method: Electron microscopy
Resolution: 3.08 Å
Organism: Homo sapiens
Chains: 20
Atoms: 15,642
Mol. weight: 479.07 kDa
Ligands: NAG
Released: 22 Oct 2025

Explore 9JY1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JY1 contains 47 α-helices and 158 β-strands across 20 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.

Chains a and A: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	30-53	24

Chains b and B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	28-54	27

Chain d: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
β-strand	26-29	4	13
β-strand	32-36	5	13
α-helix	40-41	2
β-strand	42-46	5	14
β-strand	50-51	2	13
β-strand	57-62	6	13
α-helix	63-65	3
β-strand	68-73	6	14
β-strand	84-91	8	14
β-strand	96-98	3	15
α-helix	101-125	25

Chain D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
β-strand	26-29	4	33
β-strand	32-36	5	33
β-strand	42-46	5	34
β-strand	50-51	2	33
β-strand	57-62	6	33
α-helix	63-65	3
β-strand	68-73	6	34
β-strand	84-91	8	34
β-strand	96-98	3	35
α-helix	101-125	25

Chains e and E: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37-41	5	16
β-strand	44-48	5	16
β-strand	57-61	5	14
β-strand	64-66	3	14
β-strand	75-78	4	16
β-strand	81-84	4	16
β-strand	94-100	7	14
β-strand	110-116	7	14
β-strand	122-124	3	15
α-helix	127-152	26

Chains f and F: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37-41	5	17
β-strand	44-48	5	17
β-strand	58-61	4	18
β-strand	64-65	2	18
β-strand	76-77	2	17
β-strand	81-84	4	17
β-strand	94	1	19
β-strand	96-99	4	18
β-strand	112-116	5	19
β-strand	122	1	20
α-helix	127-153	27

Chains g and G: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	21
β-strand	42-46	5	21
β-strand	54-57	4	19
β-strand	60-63	4	19
α-helix	64-66	3
β-strand	71-75	5	21
α-helix	77-79	3
β-strand	83-88	6	19
β-strand	93-102	10	19
β-strand	109	1	20
α-helix	112-139	28

Chains m and M: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	257-288	32

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab heavy chain	P, R	protein	222	Homo sapiens
Fab light chain	O, Q	protein	212	Homo sapiens
T-cell surface glycoprotein CD3 zeta chain	A, B, a, b	protein	166	Homo sapiens	P20963 (AlphaFold model)
T-cell surface glycoprotein CD3 delta chain	D, d	protein	171	Homo sapiens	P04234 (AlphaFold model)
T-cell surface glycoprotein CD3 epsilon chain	E, F, e, f	protein	207	Homo sapiens	P07766 (AlphaFold model)
T-cell surface glycoprotein CD3 gamma chain	G, g	protein	182	Homo sapiens	P09693 (AlphaFold model)
T cell receptor delta variable 2,T cell receptor delta constant	M, m	protein	292	Homo sapiens	B7Z8B9
T cell receptor gamma variable 9,T cell receptor gamma constant 1	N, n	protein	315	Homo sapiens	P0CF51, Q99603

Sequence of entity 1 (P, R), FASTA

>9JY1_1 Fab heavy chain (chains P, R)
EVQLQQSGPELVKPGASMKISCKASGYSFTGYTMNWVKQSHGKNLEWMGLINPYKGVSTY
NQKFKDKATLTVDKSSSTAYMELLSLTSEDSAVYYCARSGYYGDSDWYFDVWGQGTTLTV
FSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLK
SDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTTVDKKIVPR

Sequence of entity 2 (O, Q), FASTA

>9JY1_2 Fab light chain (chains O, Q)
DIQMTQTTSSLSASLGDRVTISCRASQDIRNYLNWYQQKPDGTVKLLIYYTSRLHSGVPS
KFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFAGGTKLEIKRADAAPTVSIFPP
ASEQLTSGGASVVCFLNNFYPKSINSKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKNEYERHNSYTCEATHKTSTSPIVKSFNRS

Sequence of entity 3 (A, B, a, b), FASTA

>9JY1_3 T-cell surface glycoprotein CD3 zeta chain (chains A, B, a, b)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRSA

Sequence of entity 4 (D, d), FASTA

>9JY1_4 T-cell surface glycoprotein CD3 delta chain (chains D, d)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Sequence of entity 5 (E, F, e, f), FASTA

>9JY1_5 T-cell surface glycoprotein CD3 epsilon chain (chains E, F, e, f)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 6 (G, g), FASTA

>9JY1_6 T-cell surface glycoprotein CD3 gamma chain (chains G, g)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RN

Sequence of entity 7 (M, m), FASTA

>9JY1_7 T cell receptor delta variable 2,T cell receptor delta constant (chains M, m)
MQRISSLIHLSLFWAGVMSAIELVPEHQTVPVSIGVPATLRCSMKGEAIGNYYINWYRKT
QGNTMTFIYREKDIYGPGFKDNFQGDIDIAKNLAVLKILAPSERDEGSYYCACDTLGMGG
EYTDKLIFGKGTRVTVEPRSQPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKIT
EFDPAIVISPSGKYNAVKLGKYEDSNSVTCSVQHDNKTVHSTDFEVKTDSTDHVKPKETE
NTKQPSKSCHKPKAIVHTEKVNMMSLTVLGLRMLFAKTVAVNFLLTAKLFFL

Sequence of entity 8 (N, n), FASTA

>9JY1_8 T cell receptor gamma variable 9,T cell receptor gamma constant 1 (chains N, n)
MLSLLHTSTLAVLGALCVYGAGHLEQPQISSTKTLSKTARLECVVSGITISATSVYWYRE
RPGEVIQFLVSISYDGTVRKESGIPSGKFEVDRIPETSTSTLTIHNVEKQDIATYYCALW
EAQQELGKKIKVFGPGTKLIITDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFF
PDVIKIHWEEKKSNTILGSQEGNTMKTNDTYMKFSWLTVPEKSLDKEHRCIVRHENNKNG
VDQEIIFPPIKTDVITMDPKDNCSKDANDTLLLQLTNTSAYYMYLLLLLKSVVYFAIITC
CLLRRTAFCCNGEKS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structures of the apo and agonist-crosslinked human gamma delta T-cell receptor. Wang, L., Li, Z., Fan, Y. et al. To be published.

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
7FJF 3.1 Å, Cryo-EM structure of a membrane protein(CS)
8TW6 3.1 Å, TCR in nanodisc ND-II
9IRU 3.14 Å, Cryo-em structure of TCR-4B1 complex

Browse structure collections

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