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T cell receptor delta joining 1

J region of the variable domain of T cell receptor (TR) delta chain that participates in the antigen recognition1. Gamma-delta TRs recognize a variety of self and foreign non-peptide antigens frequently expressed at the epithelial boundaries between the host and external environment, including endogenous lipids presented by MH-like protein CD1D and phosphoantigens presented by butyrophilin-like molecule BTN3A1. Upon antigen recognition induces rapid, innate-like immune responses involved in pathogen clearance and tissue repair2,3. Binding of gamma-delta TR complex to antigen triggers phosphorylation of immunoreceptor tyrosine-based activation motifs (ITAMs) in the CD3 chains by the LCK and FYN kinases, allowing the recruitment, phosphorylation, and activation of ZAP70 that facilitates phosphorylation of the scaffolding proteins LCP2 and LAT. This lead to the formation of a supramolecular signalosome that recruits the phospholipase PLCG1, resulting in calcium mobilization and ERK activation, ultimately leading to T cell expansion and differentiation into effector cells4. Gamma-delta TRs are produced through somatic rearrangement of a limited repertoire of variable (V), diversity (D), and joining (J) genes. The potential diversity of gamma-delta TRs is conferred by the unique ability to rearrange (D) genes in tandem and to utilize all three reading frames. The combinatorial diversity is considerably increased by the sequence exonuclease trimming and random nucleotide (N) region additions which occur during the V-(D)-J rearrangements5.

AlphaFold DB , UniProt , Accession A0A075B706, Species HUMAN (Homo sapiens, Human), Gene TRDJ1, Length 16 aa.

>TRDJ1_HUMAN|A0A075B706|TRDJ1
TDKLIFGKGTRVTVEP
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Site Residue pLDDT pLDDT confidence pLDDT10 pLDDT10 confidence SASA SASA [Ų] SASA10 SASA10 [Ų] RSA RSA unformatted RSA10 RSA10 unformatted Surface Surface10 (not used) Disorder (not used) Disorder Sec. str. Secondary structure Isomer Phi (φ) Psi (ψ) Omega (ω) Chi 1 (χ1) Chi 2 (χ2) Chi 3 (χ3) Chi 4 (χ4) Chi 5 (χ5) Tau (τ) Contacts (colored by PAE) Contact details
1T65Low85.2Confident170 Ų170155 Ų155100%1.04382%0.821SS**  092.30-47.50000107.8K3T1-K3 PolarHBondContact O-N 3.44Å; T1-K3 VanDerWaalsContact O-N 3.17Å
2D79Confident85.9Confident168 Ų168152.3 Ų152.390%0.89881%0.814SS**  trans-73.3109.2-179.9-63.3-41.8000108.5
3K79.2Confident86.6Confident179 Ų179148.9 Ų148.978%0.77880%0.803SS**PPolyproline II helixtrans-85.4123.2177.7-72.2-174.4178.9-176.10108.3T1 I5T1-K3 PolarHBondContact O-N 3.44Å; T1-K3 VanDerWaalsContact O-N 3.17Å; K3-I5 PolarHBondContact O-N 3.17Å
4L82.6Confident86.8Confident143 Ų143147.6 Ų147.675%0.74980%0.802SS**PPolyproline II helixtrans-66.6127.7170.7-61.6173.8000109F6L4-F6 HydrophobicContact CB-CE2 3.84Å; L4-F6 HydrophobicContact CB-CZ 3.91Å; L4-F6 HydrophobicContact CD1-CZ 4.26Å
5I83.9Confident86.9Confident161 Ų161148.4 Ų148.483%0.82680%0.798SS**PPolyproline II helixtrans-101.6122.8176.5-58.3175.5000107.8K3K3-I5 PolarHBondContact O-N 3.17Å
6F85.6Confident86.9Confident172 Ų172151.9 Ų151.975%0.75483%0.831SS**PPolyproline II helixtrans-102.1137177-60.7-82.9000110.3L4L4-F6 HydrophobicContact CB-CE2 3.84Å; L4-F6 HydrophobicContact CB-CZ 3.91Å; L4-F6 HydrophobicContact CD1-CZ 4.26Å
7G89.5Confident86.9Confident73 Ų73151.9 Ų151.975%0.75383%0.831SS**PPolyproline II helixtrans-73.9170176.300000112.8G9G7-G9 PolarHBondContact O-N 3.07Å; G7-G9 VanDerWaalsContact O-N 3.07Å
8K93.3Very high86.9Confident221 Ų221151.9 Ų151.996%0.96183%0.831SS**  trans-61.4-13.7-177.847.3-173.8168.7-179.20116
9G92.1Very high86.9Confident57 Ų57151.9 Ų151.959%0.58883%0.831SS**  trans64.8169.4-172.900000112.9G7G7-G9 PolarHBondContact O-N 3.07Å; G7-G9 VanDerWaalsContact O-N 3.07Å
10T93.9Very high86.9Confident135 Ų135151.9 Ų151.983%0.82883%0.831SS**  trans-135138.9173.5-56.80000108.4V12T10-V12 PolarHBondContact O-N 3.48Å
11R92.7Very high86.9Confident226 Ų226151.9 Ų151.985%0.85383%0.831SS**  trans-72.7126.9175.7-175.2179.2-60.9-91.1-2.4109.4
12V94.3Very high88.3Confident122 Ų122150.7 Ų150.774%0.73982%0.817SS**  trans-109125.5171.6-177.10000107.5T10 V14T10-V12 PolarHBondContact O-N 3.48Å; V12-V14 HydrophobicContact CG1-CG2 4.15Å
13T94.2Very high89Confident109 Ų109149.4 Ų149.467%0.66981%0.811SS**  trans-108.3125.3172.8-530000107.3
14V89.4Confident89.8Confident130 Ų130147.2 Ų147.279%0.78881%0.814SS**  trans-114.5120.8174.5-175.40000106.7V12V12-V14 HydrophobicContact CG1-CG2 4.15Å
15E88.5Confident90.4Very high160 Ų160147.5 Ų147.575%0.74882%0.819SS**  trans-92.3152.9172.4-66.9-174173.700109.6
16P86.8Confident90.9Very high204 Ų204146.3 Ų146.3100%1.32582%0.819SS**  trans-52.40-176.6-24.934.1000114.6

Retrieved 16 of 16 residues in 16.5 ms (Link to these results)