9JY4: Gamma epsilon/gamma epsilon Fab-TCR tetramer

gamma epsilon/gamma epsilon Fab-TCR tetramer. Determined by electron microscopy at 3.29 Å resolution. Released 15 Apr 2026.

Method: Electron microscopy
Resolution: 3.29 Å
Organism: Homo sapiens
Chains: 20
Atoms: 15,642
Mol. weight: 478.18 kDa
Released: 15 Apr 2026

Explore 9JY4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JY4 contains 55 α-helices and 152 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: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-33	5
α-helix	34-53	20

Chains b and B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	28-53	26

Chains d and D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
β-strand	27-28	2	1
β-strand	33-34	2	1
β-strand	42-43	2	2
β-strand	50	1	3
β-strand	59	1	3
β-strand	70-72	3	2
β-strand	85-91	7	2
β-strand	96-98	3	4
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	38-41	4	5
β-strand	44-48	5	5
β-strand	57-61	5	6
β-strand	64-65	2	6
β-strand	75-77	3	5
β-strand	81-84	4	5
β-strand	96-100	5	6
β-strand	110-116	7	2
β-strand	122-124	3	4
α-helix	127-152	26

Chain f: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37-41	5	7
β-strand	44-48	5	7
β-strand	57-61	5	8
β-strand	65-66	2	8
β-strand	77	1	7
β-strand	81-84	4	7
β-strand	94-100	7	8
α-helix	105-107	3
β-strand	111-116	6	8
β-strand	122-123	2	9
α-helix	127-153	27

Chain F: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37-41	5	28
β-strand	44-48	5	28
β-strand	57-61	5	29
β-strand	65-66	2	29
β-strand	77	1	28
β-strand	81-84	4	28
β-strand	94-100	7	29
α-helix	105-107	3
β-strand	111-116	6	29
β-strand	122-124	3	30
α-helix	127-153	27

Chain g: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	10
β-strand	42-46	5	10
β-strand	54-57	4	8
β-strand	60-61	2	8
α-helix	63-66	4
α-helix	71	1
β-strand	72-75	4	10
α-helix	77-79	3
β-strand	84-88	5	8
β-strand	93	1	8
α-helix	94-96	3
β-strand	97-102	6	8
β-strand	108-109	2	9
α-helix	112-139	28

Chain G: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	31
β-strand	42-46	5	31
β-strand	54-57	4	29
β-strand	60-61	2	29
α-helix	63-66	4
α-helix	71	1
β-strand	72-75	4	31
α-helix	77-79	3
β-strand	84-88	5	29
β-strand	93	1	29
α-helix	94-96	3
β-strand	97-102	6	29
β-strand	107-109	3	30
α-helix	112-139	28

5 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
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
Fab heavy chain	P, R	protein	222	Homo sapiens
Fab light chain	O, Q	protein	212	Homo sapiens

Sequence of entity 1 (A, B, a, b), FASTA

>9JY4_1 T-cell surface glycoprotein CD3 zeta chain (chains A, B, a, b)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRSA

Sequence of entity 2 (D, d), FASTA

>9JY4_2 T-cell surface glycoprotein CD3 delta chain (chains D, d)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Sequence of entity 3 (E, F, e, f), FASTA

>9JY4_3 T-cell surface glycoprotein CD3 epsilon chain (chains E, F, e, f)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 4 (G, g), FASTA

>9JY4_4 T-cell surface glycoprotein CD3 gamma chain (chains G, g)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RN

Sequence of entity 5 (M, m), FASTA

>9JY4_5 T cell receptor delta variable 2, T cell receptor delta constant (chains M, m)
MQRISSLIHLSLFWAGVMSAIELVPEHQTVPVSIGVPATLRCSMKGEAIGNYYINWYRKT
QGNTMTFIYREKDIYGPGFKDNFQGDIDIAKNLAVLKILAPSERDEGSYYCACDTLGMGG
EYTDKLIFGKGTRVTVEPRSQPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKIT
EFDPAIVISPSGKYNAVKLGKYEDSNSVTCSVQHDNKTVHSTDFEVKTDSTDHVKPKETE
NTKQPSKSCHKPKAIVHTEKVNMMSLTVLGLRMLFAKTVAVNFLLTAKLFFL

Sequence of entity 6 (N, n), FASTA

>9JY4_6 T cell receptor gamma variable 9,T cell receptor gamma constant 1 (chains N, n)
MLSLLHTSTLAVLGALCVYGAGHLEQPQISSTKTLSKTARLECVVSGITISATSVYWYRE
RPGEVIQFLVSISYDGTVRKESGIPSGKFEVDRIPETSTSTLTIHNVEKQDIATYYCALW
EAQQELGKKIKVFGPGTKLIITDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFF
PDVIKIHWEEKKSNTILGSQEGNTMKTNDTYMKFSWLTVPEKSLDKEHRCIVRHENNKNG
VDQEIIFPPIKTDVITMDPKDNCSKDANDTLLLQLTNTSAYYMYLLLLLKSVVYFAIITC
CLLRRTAFCCNGEKS

Sequence of entity 7 (P, R), FASTA

>9JY4_7 Fab heavy chain (chains P, R)
EVQLQQSGPELVKPGASMKISCKASGYSFTGYTMNWVKQSHGKNLEWMGLINPYKGVSTY
NQKFKDKATLTVDKSSSTAYMELLSLTSEDSAVYYCARSGYYGDSDWYFDVWGQGTTLTV
FSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLK
SDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTTVDKKIVPR

Sequence of entity 8 (O, Q), FASTA

>9JY4_8 Fab light chain (chains O, Q)
DIQMTQTTSSLSASLGDRVTISCRASQDIRNYLNWYQQKPDGTVKLLIYYTSRLHSGVPS
KFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFAGGTKLEIKRADAAPTVSIFPP
ASEQLTSGGASVVCFLNNFYPKSINSKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKNEYERHNSYTCEATHKTSTSPIVKSFNRS

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
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

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