9JXZ: V gamma9 V delta2 TCR and CD3 complex
V gamma9 V delta2 TCR and CD3 complex. Determined by electron microscopy at 3.31 Å resolution. Released 22 Oct 2025.
- Method
- Electron microscopy
- Resolution
- 3.31 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 4,846
- Mol. weight
- 193.92 kDa
- Ligands
- LPE, CLR
- Released
- 22 Oct 2025
Explore 9JXZ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9JXZ contains 12 α-helices and 40 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 | 31-53 | 23 | |
Chain b: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-54 | 27 | |
Chain d: 1 helix, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27-28 | 2 | 1 |
| β-strand | 33-34 | 2 | 1 |
| β-strand | 45 | 1 | 2 |
| β-strand | 50 | 1 | 1 |
| β-strand | 59 | 1 | 1 |
| β-strand | 70 | 1 | 2 |
| β-strand | 71 | 1 | 3 |
| β-strand | 85-86 | 2 | 3 |
| β-strand | 89-91 | 3 | 4 |
| β-strand | 96-98 | 3 | 5 |
| α-helix | 101-125 | 25 | |
Chain e: 2 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-36 | 3 | |
| β-strand | 37-41 | 5 | 6 |
| β-strand | 44-48 | 5 | 6 |
| β-strand | 57-61 | 5 | 7 |
| β-strand | 64-66 | 3 | 7 |
| β-strand | 75-77 | 3 | 6 |
| β-strand | 81-84 | 4 | 6 |
| β-strand | 95-100 | 6 | 7 |
| β-strand | 110-111 | 2 | 3 |
| β-strand | 112-113 | 2 | 7 |
| β-strand | 114-116 | 3 | 4 |
| β-strand | 122-124 | 3 | 5 |
| α-helix | 127-152 | 26 | |
Chain f: 2 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 38-41 | 4 | 8 |
| β-strand | 44-48 | 5 | 8 |
| β-strand | 57-61 | 5 | 9 |
| β-strand | 64-65 | 2 | 9 |
| β-strand | 77 | 1 | 8 |
| β-strand | 81-84 | 4 | 8 |
| β-strand | 94-95 | 2 | 10 |
| β-strand | 96-100 | 5 | 9 |
| α-helix | 105-107 | 3 | |
| β-strand | 112-116 | 5 | 10 |
| β-strand | 122-124 | 3 | 11 |
| α-helix | 127-152 | 26 | |
Chain g: 3 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-34 | 4 | 12 |
| β-strand | 42-46 | 5 | 12 |
| β-strand | 54-55 | 2 | 10 |
| β-strand | 56 | 1 | 13 |
| β-strand | 61 | 1 | 13 |
| α-helix | 64-66 | 3 | |
| β-strand | 71-75 | 5 | 12 |
| α-helix | 77-79 | 3 | |
| β-strand | 84-88 | 5 | 10 |
| β-strand | 93-102 | 10 | 10 |
| β-strand | 107-109 | 3 | 11 |
| α-helix | 112-139 | 28 | |
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 | 252-287 | 36 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| T-cell surface glycoprotein CD3 zeta chain | a, b | protein | 166 | 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) |
| T cell receptor delta variable 2,T cell receptor delta constant | m | protein | 292 | Homo sapiens | B7Z8B9 |
| T cell receptor gamma variable 9,T cell receptor gamma constant 1 | n | protein | 315 | Homo sapiens | P0CF51, Q99603 |
Sequence of entity 1 (a, b), FASTA
>9JXZ_1 T-cell surface glycoprotein CD3 zeta chain (chains a, b)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRSA
Sequence of entity 2 (d), FASTA
>9JXZ_2 T-cell surface glycoprotein CD3 delta chain (chains d)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK
Sequence of entity 3 (e, f), FASTA
>9JXZ_3 T-cell surface glycoprotein CD3 epsilon chain (chains e, f)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI
Sequence of entity 4 (g), FASTA
>9JXZ_4 T-cell surface glycoprotein CD3 gamma chain (chains g)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RN
Sequence of entity 5 (m), FASTA
>9JXZ_5 T cell receptor delta variable 2,T cell receptor delta constant (chains m)
MQRISSLIHLSLFWAGVMSAIELVPEHQTVPVSIGVPATLRCSMKGEAIGNYYINWYRKT
QGNTMTFIYREKDIYGPGFKDNFQGDIDIAKNLAVLKILAPSERDEGSYYCACDTLGMGG
EYTDKLIFGKGTRVTVEPRSQPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKIT
EFDPAIVISPSGKYNAVKLGKYEDSNSVTCSVQHDNKTVHSTDFEVKTDSTDHVKPKETE
NTKQPSKSCHKPKAIVHTEKVNMMSLTVLGLRMLFAKTVAVNFLLTAKLFFL
Sequence of entity 6 (n), FASTA
>9JXZ_6 T cell receptor gamma variable 9,T cell receptor gamma constant 1 (chains n)
MLSLLHTSTLAVLGALCVYGAGHLEQPQISSTKTLSKTARLECVVSGITISATSVYWYRE
RPGEVIQFLVSISYDGTVRKESGIPSGKFEVDRIPETSTSTLTIHNVEKQDIATYYCALW
EAQQELGKKIKVFGPGTKLIITDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFF
PDVIKIHWEEKKSNTILGSQEGNTMKTNDTYMKFSWLTVPEKSLDKEHRCIVRHENNKNG
VDQEIIFPPIKTDVITMDPKDNCSKDANDTLLLQLTNTSAYYMYLLLLLKSVVYFAIITC
CLLRRTAFCCNGEKS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| LPE | 1-O-octadecyl-sn-glycero-3-phosphocholine | C26 H57 N O6 P | 3 |
| CLR | Cholesterol | C27 H46 O | 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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