8JBV: Extracellular domain of gamma delta TCR

Extracellular domain of gamma delta TCR. Determined by electron microscopy at 3.02 Å resolution. Released 8 May 2024.

Method: Electron microscopy
Resolution: 3.02 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,624
Mol. weight: 144.15 kDa
Released: 8 May 2024

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

Secondary structure: helices and β-sheets

8JBV contains 10 α-helices and 88 β-strands across 4 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 m and M: 1 helix, 19 β-strands

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

Chain n: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	13-14	2	6
β-strand	17	1	7
β-strand	21-25	5	8
β-strand	35-41	7	6
β-strand	48-54	7	6
β-strand	59-61	3	6
β-strand	71-74	4	8
β-strand	82-86	5	8
α-helix	90-92	3
β-strand	94-99	6	6
β-strand	100-101	2	9
β-strand	113-114	2	9
β-strand	120-121	2	6
β-strand	124	1	7
β-strand	139	1	10
α-helix	145-148	4
β-strand	152-153	2	11
β-strand	155	1	10
β-strand	156-159	4	12
β-strand	167-171	5	13
α-helix	177-179	3
β-strand	181	1	14
β-strand	187-188	2	12
β-strand	193-197	5	12
β-strand	199	1	14
β-strand	200-201	2	11
β-strand	210-215	6	13
α-helix	224	1
β-strand	225	1	13
β-strand	228-229	2	13

Chain N: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	13-14	2	20
β-strand	17	1	21
β-strand	21-25	5	22
β-strand	35-41	7	20
β-strand	48-54	7	20
β-strand	59-61	3	20
β-strand	71-74	4	22
β-strand	82-86	5	22
α-helix	90-92	3
β-strand	94-99	6	20
β-strand	100-101	2	23
β-strand	113-114	2	23
β-strand	120-121	2	20
β-strand	124	1	21
β-strand	139	1	24
α-helix	145-148	4
β-strand	152-153	2	25
β-strand	155	1	24
β-strand	156-159	4	26
β-strand	167-171	5	27
α-helix	177-179	3
β-strand	187-188	2	26
β-strand	193-197	5	26
β-strand	200-201	2	25
β-strand	210-215	6	27
α-helix	223-224	2
β-strand	225	1	27
β-strand	228-229	2	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T cell receptor delta variable 1,T cell receptor delta constant	M, m	protein	307	Homo sapiens	A0A1B0GX56 (AlphaFold model), B7Z8K6 (AlphaFold model)
T cell receptor gamma variable 5,T cell receptor gamma constant 1	N, n	protein	331	Homo sapiens	A0A0B4J1U4 (AlphaFold model), P0CF51 (AlphaFold model)

Sequence of entity 1 (M, m), FASTA

>8JBV_1 T cell receptor delta variable 1,T cell receptor delta constant (chains M, m)
MDMRVPAQLLGLLLLWLSGARCMDYKDDDDKGGSETGAQKVTQAQSSVSMPVRKAVTLNC
LYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKSGRYSVNFKKAAKSVALTISALQL
EDSAKYFCALGDPGGLNTDKLIFGKGTRVTVEPRSQPHTKPSVFVMKNGTNVACLVKEFY
PKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLGKYEDSNSVTCSVQHDNKTVHSTDFE
VKTDSTDHVKPKETENTKQPSKSCHKPKAIVHTEKVNMMSLTVLGLRMLFAKTVAVNFLL
TAKLFFL

Sequence of entity 2 (N, n), FASTA

>8JBV_2 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 A0A1B0GX56 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7RYL 2.0 Å, T cell receptor CO3
7RYN 2.7 Å, CD1a-sulfatide-gdTCR complex
7RYO 3.0 Å, CD1a-dideoxymycobactin-gdTCR complex
7RYM 3.2 Å, CD1a-endo-gdTCR complex
8WXE 4.0 Å, Vgamma5Vdelta1 EH TCR-CD3 complex
8JCB 9.5 Å, Vgamma5 Vdelta1 T cell receptor complex

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