8WY0: T-cell surface glycoprotein CD3 zeta chain
T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A. Determined by electron microscopy at 3.8 Å resolution. Released 8 May 2024.
- Method
- Electron microscopy
- Resolution
- 3.8 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 4,656
- Mol. weight
- 201.54 kDa
- Ligands
- CLR
- Released
- 8 May 2024
Explore 8WY0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8WY0 contains 11 α-helices and 39 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 | 28-51 | 24 | |
Chain b: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-55 | 25 | |
Chain d: 1 helix, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-28 | 3 | 1 |
| β-strand | 32-36 | 5 | 1 |
| β-strand | 42-46 | 5 | 2 |
| β-strand | 50 | 1 | 1 |
| β-strand | 57-62 | 6 | 1 |
| β-strand | 69-72 | 4 | 2 |
| β-strand | 73 | 1 | 3 |
| β-strand | 84 | 1 | 3 |
| β-strand | 85-91 | 7 | 2 |
| β-strand | 96-97 | 2 | 4 |
| α-helix | 103-125 | 23 | |
Chain e: 1 helix, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 37-41 | 5 | 5 |
| β-strand | 44-48 | 5 | 5 |
| β-strand | 58-61 | 4 | 2 |
| β-strand | 65 | 1 | 2 |
| β-strand | 77 | 1 | 5 |
| β-strand | 82-84 | 3 | 5 |
| β-strand | 95-99 | 5 | 2 |
| β-strand | 110-116 | 7 | 2 |
| β-strand | 123-124 | 2 | 4 |
| α-helix | 128-151 | 24 | |
Chain f: 3 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 37-41 | 5 | 6 |
| β-strand | 44-48 | 5 | 6 |
| β-strand | 57 | 1 | 7 |
| β-strand | 60 | 1 | 8 |
| β-strand | 65 | 1 | 8 |
| β-strand | 75 | 1 | 6 |
| β-strand | 81-84 | 4 | 6 |
| β-strand | 95 | 1 | 9 |
| β-strand | 100 | 1 | 7 |
| α-helix | 105-107 | 3 | |
| β-strand | 113-114 | 2 | 9 |
| α-helix | 116-118 | 3 | |
| β-strand | 122-124 | 3 | 10 |
| α-helix | 127-153 | 27 | |
Chain g: 2 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-33 | 3 | 11 |
| β-strand | 42-43 | 2 | 12 |
| β-strand | 44-46 | 3 | 11 |
| β-strand | 55-57 | 3 | 13 |
| β-strand | 61 | 1 | 13 |
| β-strand | 73-75 | 3 | 12 |
| α-helix | 77-79 | 3 | |
| β-strand | 85-87 | 3 | 13 |
| β-strand | 99-100 | 2 | 9 |
| β-strand | 107-109 | 3 | 10 |
| α-helix | 115-134 | 20 | |
Chain m: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 261-290 | 30 | |
Chain n: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 272-306 | 35 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| T-cell surface glycoprotein CD3 zeta chain | a, b | protein | 195 | 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) |
| Signal peptide,flag tag,T cell receptor delta variable 2,T cell receptor delta constant | m | protein | 310 | Homo sapiens | A0JD36, B7Z8K6 |
| Signal peptide,flag tag,T cell receptor gamma variable 9,T cell receptor gamma constant 1 | n | protein | 332 | Homo sapiens | P0CF51, Q99603 |
Sequence of entity 1 (a, b), FASTA
>8WY0_1 T-cell surface glycoprotein CD3 zeta chain (chains a, b)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRAAAWSHPQFEKGGGSG
GGSGGSAWSHPQFEK
Sequence of entity 2 (d), FASTA
>8WY0_2 T-cell surface glycoprotein CD3 delta chain (chains d)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK
Sequence of entity 3 (e, f), FASTA
>8WY0_3 T-cell surface glycoprotein CD3 epsilon chain (chains e, f)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI
Sequence of entity 4 (g), FASTA
>8WY0_4 T-cell surface glycoprotein CD3 gamma chain (chains g)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RN
Sequence of entity 5 (m), FASTA
>8WY0_5 Signal peptide,flag tag,T cell receptor delta variable 2,T cell receptor delta constant (chains m)
MDMRVPAQLLGLLLLWLSGARCMDYKDDDDKGGSETGAIELVPEHQTVPVSIGVPATLRC
SMKGEAIGNYYINWYRKTQGNTMTFIYREKDIYGPGFKDNFQGDIDIAKNLAVLKILAPS
ERDEGSYYCACDTLGMGGEYTDKLIFGKGTRVTVEPRSQPHTKPSVFVMKNGTNVACLVK
EFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLGKYEDSNSVTCSVQHDNKTVHST
DFEVKTDSTDHVKPKETENTKQPSKSCHKPKAIVHTEKVNMMSLTVLGLRMLFAKTVAVN
ALLTAKLAAL
Sequence of entity 6 (n), FASTA
>8WY0_6 Signal peptide,flag tag,T cell receptor gamma variable 9,T cell receptor gamma constant 1 (chains n)
MDMRVPAQLLGLLLLWLSGARCMDYKDDDDKGGSETGAGHLEQPQISSTKTLSKTARLEC
VVSGITISATSVYWYRERPGEVIQFLVSISYDGTVRKESGIPSGKFEVDRIPETSTSTLT
IHNVEKQDIATYYCALWEAQQELGKKIKVFGPGTKLIITDKQLDADVSPKPTIFLPSIAE
TKLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILGSQEGNTMKTNDTYMKFSWLTVPEKS
LDKEHRCIVRHENNKNGVDQEIIFPPIKTDVITMDPKDNCSKDANDTLLLQLTNTSAYYM
YLLLLLKSVVYFAIITCCLLRRTAFCCNGEKS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CLR | Cholesterol | C27 H46 O | 1 |
Primary citation
Structures of human gamma delta T cell receptor-CD3 complex. Xin, W., Huang, B., Chi, X. et al. Nature (2024) 630:222-229. DOI 10.1038/s41586-024-07439-4 · PubMed
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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