9JY2: Fab-CD3-delta epsilon-TCR complex
Fab-CD3-delta epsilon-TCR complex. Determined by electron microscopy at 3.24 Å resolution. Released 26 Nov 2025.
- Method
- Electron microscopy
- Resolution
- 3.24 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 6,515
- Mol. weight
- 93.83 kDa
- Ligands
- CLR, NAG
- Released
- 26 Nov 2025
Explore 9JY2 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9JY2 contains 22 α-helices and 61 β-strands across 10 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, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-6 | 3 | 12 |
| β-strand | 10 | 1 | 13 |
| β-strand | 19-25 | 7 | 12 |
| β-strand | 33-38 | 6 | 13 |
| β-strand | 44-49 | 6 | 13 |
| β-strand | 53-54 | 2 | 13 |
| α-helix | 55 | 1 | |
| β-strand | 64-67 | 4 | 12 |
| β-strand | 70-75 | 6 | 12 |
| β-strand | 85-90 | 6 | 13 |
| α-helix | 96 | 1 | |
| β-strand | 97 | 1 | 14 |
| β-strand | 102-103 | 2 | 13 |
Chain b: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-54 | 27 | |
Chain B: 3 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 15 |
| β-strand | 12 | 1 | 16 |
| β-strand | 17-25 | 9 | 15 |
| α-helix | 29-31 | 3 | |
| β-strand | 32-40 | 9 | 14 |
| β-strand | 44-52 | 9 | 14 |
| β-strand | 57-60 | 4 | 14 |
| α-helix | 62-64 | 3 | |
| β-strand | 68-73 | 6 | 15 |
| β-strand | 78-84 | 7 | 15 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-100 | 9 | 14 |
| β-strand | 111-112 | 2 | 14 |
| β-strand | 116-118 | 3 | 14 |
| β-strand | 120 | 1 | 16 |
Chain d: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-29 | 4 | 1 |
| β-strand | 32-36 | 5 | 1 |
| α-helix | 40 | 1 | |
| β-strand | 41-46 | 6 | 2 |
| β-strand | 50-51 | 2 | 1 |
| β-strand | 57-62 | 6 | 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 | 101-125 | 25 | |
Chain e: 3 helices, 9 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 | 64-66 | 3 | 2 |
| β-strand | 75-78 | 4 | 4 |
| β-strand | 81-84 | 4 | 4 |
| α-helix | 89-92 | 4 | |
| β-strand | 94-100 | 7 | 2 |
| β-strand | 110-116 | 7 | 2 |
| β-strand | 122-124 | 3 | 3 |
| α-helix | 127-152 | 26 | |
Chain f: 3 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-36 | 3 | |
| β-strand | 37-41 | 5 | 5 |
| β-strand | 44-48 | 5 | 5 |
| β-strand | 58-61 | 4 | 6 |
| β-strand | 64-66 | 3 | 6 |
| β-strand | 76-77 | 2 | 5 |
| β-strand | 82-84 | 3 | 5 |
| β-strand | 94 | 1 | 7 |
| β-strand | 96-99 | 4 | 6 |
| β-strand | 112-116 | 5 | 7 |
| β-strand | 122-124 | 3 | 8 |
| α-helix | 125-126 | 2 | |
| α-helix | 127-153 | 27 | |
Chain g: 4 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-34 | 4 | 9 |
| β-strand | 42-46 | 5 | 9 |
| β-strand | 55-57 | 3 | 10 |
| β-strand | 60-63 | 4 | 10 |
| α-helix | 64-66 | 3 | |
| β-strand | 72-75 | 4 | 9 |
| α-helix | 77-79 | 3 | |
| β-strand | 83 | 1 | 7 |
| β-strand | 85-86 | 2 | 10 |
| β-strand | 87-88 | 2 | 11 |
| β-strand | 93-94 | 2 | 11 |
| α-helix | 95-96 | 2 | |
| β-strand | 98-102 | 5 | 7 |
| β-strand | 107-109 | 3 | 8 |
| α-helix | 112-139 | 28 | |
2 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 | protein | 31 | Homo sapiens | P20963 (AlphaFold model) |
| T-cell surface glycoprotein CD3 delta chain | d | protein | 105 | Homo sapiens | P04234 (AlphaFold model) |
| T-cell surface glycoprotein CD3 epsilon chain | e, f | protein | 122 | Homo sapiens | P07766 (AlphaFold model) |
| T-cell surface glycoprotein CD3 gamma chain | g | protein | 115 | Homo sapiens | P09693 (AlphaFold model) |
| T cell receptor delta constant | m | protein | 36 | Homo sapiens | B7Z8K6 |
| T cell receptor gamma constant 1 | n | protein | 38 | Homo sapiens | P0CF51 |
| Fab light chain | A | protein | 104 | Homo sapiens | |
| Fab heavy chain | B | protein | 121 | Homo sapiens | |
Sequence of entity 1 (a, b), FASTA
>9JY2_1 T-cell surface glycoprotein CD3 zeta chain (chains a, b)
LLDPKLCYLLDGILFIYGVILTALFLRVKFS
Sequence of entity 2 (d), FASTA
>9JY2_2 T-cell surface glycoprotein CD3 delta chain (chains d)
FKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDLGKRILDPRGIYRCNGTDIYKD
KESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLALGVFCFA
Sequence of entity 3 (e, f), FASTA
>9JY2_3 T-cell surface glycoprotein CD3 epsilon chain (chains e, f)
QTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQ
SGYYVCYPRGSKPEDANFYLYLRARVCENCMEMDVMSVATIVIVDICITGGLLLLVYYWS
KN
Sequence of entity 4 (g), FASTA
>9JY2_4 T-cell surface glycoprotein CD3 gamma chain (chains g)
KGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSNAKDPRGMY
QCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLFAEIVSIFVLAVGVYFIAGQD
Sequence of entity 5 (m), FASTA
>9JY2_5 T cell receptor delta constant (chains m)
VHTEKVNMMSLTVLGLRMLFAKTVAVNFLLTAKLFF
Sequence of entity 6 (n), FASTA
>9JY2_6 T cell receptor gamma constant 1 (chains n)
DTLLLQLTNTSAYYMYLLLLLKSVVYFAIITCCLLRRT
Sequence of entity 7 (A), FASTA
>9JY2_7 Fab light chain (chains A)
DIQMTQTTSSLSASLGDRVTISCRASQDIRNYLNWYQQKPDGTVKLLIYYTSRLHSGVPS
KFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFAGGTKL
Sequence of entity 8 (B), FASTA
>9JY2_8 Fab heavy chain (chains B)
EVQLQQSGPELVKPGASMKISCKASGYSFTGYTMNWVKQSHGKNLEWMGLINPYKGVSTY
NQKFKDKATLTVDKSSSTAYMELLSLTSEDSAVYYCARSGYYGDSDWYFDVWGQGTTLTV
F
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CLR | Cholesterol | C27 H46 O | 1 |
| 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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