8WYI: T-cell surface glycoprotein CD3 zeta chain
T cell receptor delta 2 gamma 9 with TCRD TM domain chimera of TRAC. Determined by electron microscopy at 3.9 Å resolution. Released 8 May 2024.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 4,659
- Mol. weight
- 201.38 kDa
- Released
- 8 May 2024
Explore 8WYI in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8WYI contains 9 α-helices and 36 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 | 28-54 | 27 | |
Chain b: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-53 | 25 | |
Chain d: 1 helix, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 28 | 1 | 1 |
| β-strand | 32 | 1 | 2 |
| β-strand | 33 | 1 | 1 |
| β-strand | 41 | 1 | 3 |
| β-strand | 45-46 | 2 | 4 |
| β-strand | 62 | 1 | 2 |
| β-strand | 68-70 | 3 | 4 |
| β-strand | 73 | 1 | 3 |
| β-strand | 84 | 1 | 3 |
| β-strand | 85-89 | 5 | 4 |
| β-strand | 96-97 | 2 | 5 |
| α-helix | 101-126 | 26 | |
Chain e: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 37-41 | 5 | 6 |
| β-strand | 44-48 | 5 | 6 |
| β-strand | 57 | 1 | 7 |
| α-helix | 71-73 | 3 | |
| β-strand | 76-77 | 2 | 6 |
| β-strand | 82-84 | 3 | 6 |
| β-strand | 100 | 1 | 7 |
| β-strand | 110-113 | 4 | 4 |
| β-strand | 123-124 | 2 | 5 |
| α-helix | 127-151 | 25 | |
Chain f: 1 helix, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 37-41 | 5 | 8 |
| β-strand | 44-48 | 5 | 8 |
| β-strand | 58-60 | 3 | 9 |
| β-strand | 61 | 1 | 10 |
| β-strand | 64 | 1 | 10 |
| β-strand | 84 | 1 | 8 |
| β-strand | 94 | 1 | 11 |
| β-strand | 97-99 | 3 | 9 |
| β-strand | 114-116 | 3 | 11 |
| α-helix | 127-153 | 27 | |
Chain g: 1 helix, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 32-34 | 3 | 12 |
| β-strand | 42 | 1 | 13 |
| β-strand | 43-45 | 3 | 12 |
| β-strand | 55 | 1 | 14 |
| β-strand | 63 | 1 | 14 |
| β-strand | 75 | 1 | 13 |
| β-strand | 87 | 1 | 14 |
| β-strand | 100-102 | 3 | 11 |
| α-helix | 114-136 | 23 | |
Chain m: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 261-289 | 29 | |
Chain n: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 272-304 | 33 | |
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,T cell… | m | protein | 310 | Homo sapiens | A0JD36, B7Z8K6, P01848 |
| Signal peptide,flag tag,T cell receptor gamma variable 9,T cell receptor gamma constant 1,T cell… | n | protein | 332 | Homo sapiens | P0CF51, Q99603 |
Sequence of entity 1 (a, b), FASTA
>8WYI_1 T-cell surface glycoprotein CD3 zeta chain (chains a, b)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRAAAWSHPQFEKGGGSG
GGSGGSAWSHPQFEK
Sequence of entity 2 (d), FASTA
>8WYI_2 T-cell surface glycoprotein CD3 delta chain (chains d)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK
Sequence of entity 3 (e, f), FASTA
>8WYI_3 T-cell surface glycoprotein CD3 epsilon chain (chains e, f)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI
Sequence of entity 4 (g), FASTA
>8WYI_4 T-cell surface glycoprotein CD3 gamma chain (chains g)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RN
Sequence of entity 5 (m), FASTA
>8WYI_5 Signal peptide,flag tag,T cell receptor delta variable 2,T cell receptor delta constant,T cell receptor alpha chain constant,T cell receptor delta variable 2,T cell receptor delta constant,T cell receptor alpha chain constant (chains m)
MDMRVPAQLLGLLLLWLSGARCMDYKDDDDKGGSETGAIELVPEHQTVPVSIGVPATLRC
SMKGEAIGNYYINWYRKTQGNTMTFIYREKDIYGPGFKDNFQGDIDIAKNLAVLKILAPS
ERDEGSYYCACDTLGMGGEYTDKLIFGKGTRVTVEPRSQPHTKPSVFVMKNGTNVACLVK
EFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLGKYEDSNSVTCSVQHDNKTVHST
DFEVKTDSTDHVKPKETENTKQPSKSCHKPKAIVHTEKVNMMSLTVLGLRILLLKVAGFN
LLMTLRLWSS
Sequence of entity 6 (n), FASTA
>8WYI_6 Signal peptide,flag tag,T cell receptor gamma variable 9,T cell receptor gamma constant 1,T cell receptor gamma variable 9,T cell receptor gamma constant 1 (chains n)
MDMRVPAQLLGLLLLWLSGARCMDYKDDDDKGGSETGAGHLEQPQISSTKTLSKTARLEC
VVSGITISATSVYWYRERPGEVIQFLVSISYDGTVRKESGIPSGKFEVDRIPETSTSTLT
IHNVEKQDIATYYCALWEAQQELGKKIKVFGPGTKLIITDKQLDADVSPKPTIFLPSIAE
TKLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILGSQEGNTMKTNDTYMKFSWLTVPEKS
LDKEHRCIVRHENNKNGVDQEIIFPPIKTDVITMDPKDNCSKDANDTLLLQLTNTSAYYM
YLLLLLKSVVYFAIITCCLLRRTAFCCNGEKS
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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