9JY3: Delta epsilon/gamma epsilon Fab-TCR tetramer
delta epsilon/gamma epsilon Fab-TCR tetramer. Determined by electron microscopy at 3.35 Å resolution. Released 15 Apr 2026.
- Method
- Electron microscopy
- Resolution
- 3.35 Å
- Organism
- Homo sapiens
- Chains
- 20
- Atoms
- 15,638
- Mol. weight
- 231.3 kDa
- Ligands
- NAG
- Released
- 15 Apr 2026
Explore 9JY3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9JY3 contains 50 α-helices and 157 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.
Chain a: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-53 | 24 | |
Chain A: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-32 | 4 | |
| α-helix | 33-53 | 21 | |
Chains b and B: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-54 | 27 | |
Chain d: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-29 | 4 | 13 |
| β-strand | 32-36 | 5 | 13 |
| 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 | 68-74 | 7 | 14 |
| β-strand | 83-91 | 9 | 14 |
| β-strand | 96-98 | 3 | 15 |
| α-helix | 101-125 | 25 | |
Chain 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 | 42-45 | 4 | 2 |
| β-strand | 50 | 1 | 3 |
| β-strand | 59 | 1 | 3 |
| β-strand | 70-73 | 4 | 2 |
| β-strand | 84-91 | 8 | 2 |
| β-strand | 96-98 | 3 | 4 |
| α-helix | 101-125 | 25 | |
Chain e: 3 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 |
| α-helix | 89-92 | 4 | |
| β-strand | 94-100 | 7 | 14 |
| β-strand | 110-116 | 7 | 14 |
| β-strand | 122-124 | 3 | 15 |
| α-helix | 127-152 | 26 | |
Chain E: 2 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-37 | 4 | |
| β-strand | 38-41 | 4 | 5 |
| β-strand | 44-48 | 5 | 5 |
| β-strand | 57-61 | 5 | 2 |
| β-strand | 64-65 | 2 | 2 |
| β-strand | 75-77 | 3 | 5 |
| β-strand | 81-84 | 4 | 5 |
| β-strand | 95-100 | 6 | 2 |
| β-strand | 111-116 | 6 | 2 |
| β-strand | 122-124 | 3 | 4 |
| α-helix | 127-152 | 26 | |
Chain f: 2 helices, 9 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 | 82-84 | 3 | 17 |
| β-strand | 96-99 | 4 | 18 |
| β-strand | 112-116 | 5 | 19 |
| β-strand | 124 | 1 | 20 |
| α-helix | 127-153 | 27 | |
10 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 | 31 | Homo sapiens | P20963 (AlphaFold model) |
| T-cell surface glycoprotein CD3 delta chain | D, d | protein | 105 | Homo sapiens | P04234 (AlphaFold model) |
| T-cell surface glycoprotein CD3 epsilon chain | E, F, e, f | protein | 122 | Homo sapiens | P07766 (AlphaFold model) |
| T-cell surface glycoprotein CD3 gamma chain | G, g | protein | 115 | Homo sapiens | P09693 (AlphaFold model) |
| T cell receptor delta constant | M, m | protein | 36 | Homo sapiens | B7Z8K6 |
| T cell receptor gamma constant 1 | N, n | protein | 38 | Homo sapiens | P0CF51 |
| Fab light chain | O, Q | protein | 212 | Homo sapiens | |
| Fab heavy chain | P, R | protein | 222 | Homo sapiens | |
Sequence of entity 1 (A, B, a, b), FASTA
>9JY3_1 T-cell surface glycoprotein CD3 zeta chain (chains A, B, a, b)
LLDPKLCYLLDGILFIYGVILTALFLRVKFS
Sequence of entity 2 (D, d), FASTA
>9JY3_2 T-cell surface glycoprotein CD3 delta chain (chains D, d)
FKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDLGKRILDPRGIYRCNGTDIYKD
KESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLALGVFCFA
Sequence of entity 3 (E, F, e, f), FASTA
>9JY3_3 T-cell surface glycoprotein CD3 epsilon chain (chains E, F, e, f)
QTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQ
SGYYVCYPRGSKPEDANFYLYLRARVCENCMEMDVMSVATIVIVDICITGGLLLLVYYWS
KN
Sequence of entity 4 (G, g), FASTA
>9JY3_4 T-cell surface glycoprotein CD3 gamma chain (chains G, g)
KGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSNAKDPRGMY
QCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLFAEIVSIFVLAVGVYFIAGQD
Sequence of entity 5 (M, m), FASTA
>9JY3_5 T cell receptor delta constant (chains M, m)
VHTEKVNMMSLTVLGLRMLFAKTVAVNFLLTAKLFF
Sequence of entity 6 (N, n), FASTA
>9JY3_6 T cell receptor gamma constant 1 (chains N, n)
DTLLLQLTNTSAYYMYLLLLLKSVVYFAIITCCLLRRT
Sequence of entity 7 (O, Q), FASTA
>9JY3_7 Fab light chain (chains O, Q)
DIQMTQTTSSLSASLGDRVTISCRASQDIRNYLNWYQQKPDGTVKLLIYYTSRLHSGVPS
KFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFAGGTKLEIKRADAAPTVSIFPP
ASEQLTSGGASVVCFLNNFYPKSINSKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKNEYERHNSYTCEATHKTSTSPIVKSFNRS
Sequence of entity 8 (P, R), FASTA
>9JY3_8 Fab heavy chain (chains P, R)
EVQLQQSGPELVKPGASMKISCKASGYSFTGYTMNWVKQSHGKNLEWMGLINPYKGVSTY
NQKFKDKATLTVDKSSSTAYMELLSLTSEDSAVYYCARSGYYGDSDWYFDVWGQGTTLTV
FSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLK
SDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTTVDKKIVPR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
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
Browse structure collections
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