8YC0: T cell receptor V delta2 V gamma9 in GDN

T cell receptor V delta2 V gamma9 in GDN. Determined by electron microscopy at 4.12 Å resolution. Released 8 May 2024.

Method: Electron microscopy
Resolution: 4.12 Å
Organism: Homo sapiens
Chains: 8
Atoms: 4,635
Mol. weight: 201.76 kDa
Ligands: CLR
Released: 8 May 2024

Explore 8YC0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YC0 contains 11 α-helices and 30 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	27-49	23

Chain b: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-53	25

Chain d: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
β-strand	28	1	1
β-strand	32-35	4	1
β-strand	41-46	6	2
β-strand	58-62	5	1
β-strand	68-73	6	2
β-strand	84-90	7	2
β-strand	96-98	3	3
α-helix	101-123	23

Chain e: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	37-41	5	4
β-strand	44-48	5	4
β-strand	58-61	4	2
β-strand	76-77	2	4
β-strand	81-84	4	4
β-strand	95-99	5	2
β-strand	110-115	6	2
β-strand	122-124	3	3
α-helix	127-151	25

Chain f: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37-38	2	5
β-strand	41	1	5
β-strand	44-48	5	5
β-strand	60	1	6
β-strand	75-77	3	5
β-strand	82-85	4	5
β-strand	97	1	6
β-strand	112-115	4	7
α-helix	127-153	27

Chain g: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	8
β-strand	42-46	5	8
β-strand	54-57	4	9
β-strand	60-64	5	9
β-strand	72-75	4	8
α-helix	77-79	3
β-strand	82-85	4	7
β-strand	97-101	5	7
α-helix	112-136	25

Chain m: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	257-288	32

Chain n: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	253-287	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)
T cell receptor delta variable 2,T cell receptor delta constant	m	protein	310	Homo sapiens	A0JD36, B7Z8K6
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

>8YC0_1 T-cell surface glycoprotein CD3 zeta chain (chains a, b)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRAAAWSHPQFEKGGGSG
GGSGGSAWSHPQFEK

Sequence of entity 2 (d), FASTA

>8YC0_2 T-cell surface glycoprotein CD3 delta chain (chains d)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Sequence of entity 3 (e, f), FASTA

>8YC0_3 T-cell surface glycoprotein CD3 epsilon chain (chains e, f)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 4 (g), FASTA

>8YC0_4 T-cell surface glycoprotein CD3 gamma chain (chains g)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RN

Sequence of entity 5 (m), FASTA

>8YC0_5 T cell receptor delta variable 2,T cell receptor delta constant (chains m)
MDMRVPAQLLGLLLLWLSGARCMDYKDDDDKGGSETGAIELVPEHQTVPVSIGVPATLRC
SMKGEAIGNYYINWYRKTQGNTMTFIYREKDIYGPGFKDNFQGDIDIAKNLAVLKILAPS
ERDEGSYYCACDTLGMGGEYTDKLIFGKGTRVTVEPRSQPHTKPSVFVMKNGTNVACLVK
EFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLGKYEDSNSVTCSVQHDNKTVHST
DFEVKTDSTDHVKPKETENTKQPSKSCHKPKAIVHTEKVNMMSLTVLGLRMLFAKTVAVN
FLLTAKLFFL

Sequence of entity 6 (n), FASTA

>8YC0_6 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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