8JCB: Vgamma5 Vdelta1 T cell receptor complex

Vgamma5 Vdelta1 T cell receptor complex. Determined by electron microscopy at 9.5 Å resolution. Released 8 May 2024.

Method: Electron microscopy
Resolution: 9.5 Å
Organism: Homo sapiens
Chains: 16
Atoms: 15,950
Mol. weight: 402.97 kDa
Released: 8 May 2024

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

Secondary structure: helices and β-sheets

8JCB contains 42 α-helices and 166 β-strands across 16 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.

Chains a and A: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	28-32	5
α-helix	39-55	17

Chains b and B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	28-51	24

Chains d and D: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	30
β-strand	33	1	30
β-strand	35-36	2	31
β-strand	42-46	5	32
β-strand	57-58	2	31
β-strand	69-73	5	32
β-strand	84-88	5	32
β-strand	89-91	3	33
β-strand	96-98	3	34
α-helix	108-125	18

Chains e and E: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	38-41	4	35
β-strand	44-48	5	35
β-strand	57	1	36
β-strand	59-60	2	37
β-strand	65-66	2	37
β-strand	77	1	35
β-strand	81-84	4	35
β-strand	100	1	36
α-helix	105-107	3
β-strand	114-116	3	33
β-strand	122-124	3	34
α-helix	128-141	14
α-helix	145-151	7

Chains f and F: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	35-36	2
β-strand	37-41	5	38
β-strand	44-48	5	38
β-strand	57-58	2	39
β-strand	59	1	40
β-strand	61	1	41
β-strand	66	1	40
β-strand	76-77	2	38
β-strand	81-84	4	38
β-strand	96	1	41
β-strand	99-100	2	39
α-helix	105-107	3
β-strand	111-114	4	42
β-strand	122-124	3	43
α-helix	133-153	21

Chains g and G: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	44
β-strand	41-46	6	44
β-strand	57	1	45
β-strand	60	1	45
β-strand	71-76	6	44
α-helix	77-79	3
β-strand	85	1	42
β-strand	97-100	4	42
β-strand	107-109	3	43
α-helix	124-139	16

Chains m and M: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	23-25	3	46
β-strand	30-34	5	47
β-strand	38-46	9	46
β-strand	53-59	7	47
β-strand	65-72	8	47
β-strand	79-80	2	46
β-strand	83-88	6	46
β-strand	93-99	7	46
β-strand	107-113	7	47
β-strand	125-126	2	47
β-strand	130-135	6	47
β-strand	146-150	5	48
β-strand	154-162	9	48
β-strand	176	1	49
β-strand	183-186	4	48
β-strand	192-199	8	48
β-strand	200	1	49
β-strand	210	1	50
α-helix	212-214	3
β-strand	217	1	50
α-helix	259-286	28

Chain n: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	13-14	2	51
β-strand	17	1	52
β-strand	21-25	5	53
β-strand	35-41	7	51
β-strand	48-54	7	51
β-strand	59-61	3	51
β-strand	71-74	4	53
β-strand	82-86	5	53
α-helix	90-92	3
β-strand	94-99	6	51
β-strand	100-101	2	54
β-strand	113-114	2	54
β-strand	120-121	2	51
β-strand	124	1	52
β-strand	139	1	55
α-helix	145-148	4
β-strand	152-153	2	56
β-strand	155	1	55
β-strand	156-159	4	57
β-strand	167-171	5	58
α-helix	177-179	3
β-strand	181	1	59
β-strand	187-188	2	57
β-strand	193-197	5	57
β-strand	199	1	59
β-strand	200-201	2	56
β-strand	210-215	6	58
α-helix	224	1
β-strand	225	1	58
β-strand	228-229	2	58
α-helix	255-260	6
α-helix	263-266	4
α-helix	273-284	12

1 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, a, b	protein	195	Homo sapiens	P20963 (AlphaFold model)
T-cell surface glycoprotein CD3 delta chain	D, d	protein	171	Homo sapiens	P04234 (AlphaFold model)
T-cell surface glycoprotein CD3 epsilon chain	E, F, e, f	protein	207	Homo sapiens	P07766 (AlphaFold model)
T-cell surface glycoprotein CD3 gamma chain	G, g	protein	182	Homo sapiens	P09693 (AlphaFold model)
T cell receptor delta variable 1,T cell receptor delta constant	M, m	protein	307	Homo sapiens	A0A1B0GX56, B7Z8K6
T cell receptor gamma variable 5,T cell receptor gamma constant 1	N, n	protein	331	Homo sapiens	A0A0B4J1U4, P0CF51

Sequence of entity 1 (A, B, a, b), FASTA

>8JCB_1 T-cell surface glycoprotein CD3 zeta chain (chains A, B, a, b)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRAAAWSHPQFEKGGGSG
GGSGGSAWSHPQFEK

Sequence of entity 2 (D, d), FASTA

>8JCB_2 T-cell surface glycoprotein CD3 delta chain (chains D, d)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Sequence of entity 3 (E, F, e, f), FASTA

>8JCB_3 T-cell surface glycoprotein CD3 epsilon chain (chains E, F, e, f)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 4 (G, g), FASTA

>8JCB_4 T-cell surface glycoprotein CD3 gamma chain (chains G, g)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RN

Sequence of entity 5 (M, m), FASTA

>8JCB_5 T cell receptor delta variable 1,T cell receptor delta constant (chains M, m)
MDMRVPAQLLGLLLLWLSGARCMDYKDDDDKGGSETGAQKVTQAQSSVSMPVRKAVTLNC
LYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKSGRYSVNFKKAAKSVALTISALQL
EDSAKYFCALGDPGGLNTDKLIFGKGTRVTVEPRSQPHTKPSVFVMKNGTNVACLVKEFY
PKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLGKYEDSNSVTCSVQHDNKTVHSTDFE
VKTDSTDHVKPKETENTKQPSKSCHKPKAIVHTEKVNMMSLTVLGLRMLFAKTVAVNFLL
TAKLFFL

Sequence of entity 6 (N, n), FASTA

>8JCB_6 T cell receptor gamma variable 5,T cell receptor gamma constant 1 (chains N, n)
MDMRVPAQLLGLLLLWLSGARCMDYKDDDDKGGSETGSSNLEGGTKSVTRPTRSSAEITC
DLTVINAFYIHWYLHQEGKAPQRLLYYDVSNSKDVLESGLSPGKYYTHTPRRWSWILILR
NLIENDSGVYYCATWDRGNPKTHYYKKLFGSGTTLVVTDKQLDADVSPKPTIFLPSIAET
KLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILGSQEGNTMKTNDTYMKFSWLTVPEKSL
DKEHRCIVRHENNKNGVDQEIIFPPIKTDVITMDPKDNCSKDANDTLLLQLTNTSAYYMY
LLLLLKSVVYFAIITCCLLRRTAFCCNGEKS

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

About this viewer

MolViewer shows 8JCB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.