SMTL ID : 7phr.1

Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-2-1-1-2-mer

Ligands

1 x TYR- LEU- GLU- PRO- GLY- PRO- VAL- THR- VAL: Tumor-associated antigentic peptide gp100(Non-covalent)

TYR-LEU-GLU-PRO-GLY-PRO-VAL-THR-VAL.1: 39 residues within 4Å: Chain A: N.31, D.93, G.94, T.96 Chain B: D.31, W.96, G.97, A.98, P.99, Y.100 Chain F: M.17, Y.19, F.21, M.57, Y.71, E.75, K.78, V.79, H.82, T.85, V.88, D.89, T.92, L.93, Y.96, R.109, Y.111, Y.128, Y.135, T.155, K.158, W.159, V.164, Q.167, L.168, Y.171, T.175, W.179, Y.183 45 PLIP interactions: 39 interactions with chain F, 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: F:Y.19, F:F.21, F:Y.71, F:K.78, F:K.78, F:V.79, F:T.85, F:V.88, F:D.89, F:T.92, F:L.93, F:Y.111, F:Y.128, F:Y.135, F:T.155, F:W.159, F:V.164, F:L.168, F:Y.171, F:Y.171, F:T.175, F:W.179, B:W.96, B:P.99, B:Y.100 Hydrogen bonds: F:Y.19, F:Y.19, F:E.75, F:K.78, F:D.89, F:R.109, F:Y.111, F:Y.111, F:T.155, F:K.158, F:Q.167, F:Y.171, F:Y.183, B:D.31, B:D.31, A:G.94 Salt bridges: F:K.158 pi-Stacking: F:W.179, F:W.179 pi-Cation interactions: F:K.78

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 2 residues within 4Å: Chain A: T.21, N.23 No protein-ligand interaction detected (PLIP) NAG.3: 2 residues within 4Å: Chain A: Q.141, N.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.141, A:Q.141, A:N.143, A:N.143 NAG.4: 2 residues within 4Å: Chain A: D.129, N.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.129, A:N.177 NAG.5: 1 residues within 4Å: Chain B: N.19 No protein-ligand interaction detected (PLIP) NAG.6: 5 residues within 4Å: Chain D: N.17, G.54, T.55, I.57, Y.58 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.17, D:T.55, D:Y.58 NAG.7: 4 residues within 4Å: Chain D: T.18, S.19, T.21, N.53 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.18 Hydrogen bonds: D:T.18, D:N.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Susac, L. et al., Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC. Cell (2022)

Release Date

2022-08-31

Peptides

T-cell receptor alpha chain: A
T-cell receptor beta chain: B
T-cell surface glycoprotein CD3 gamma chain: C
T-cell surface glycoprotein CD3 delta chain, green fluorescent protein: D
T-cell surface glycoprotein CD3 epsilon chain: EI
HLA class I histocompatibility antigen, A alpha chain: F
Beta-2-microglobulin: G
T-cell surface glycoprotein CD3 zeta chain: HJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

I
e

F
H

G
L

H
Z

J
z

Membrane

We predict this structure to be a membrane protein.
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T-cell receptor alpha chain

T-cell receptor beta chain

T-cell surface glycoprotein CD3 gamma chain

T-cell surface glycoprotein CD3 delta chain, green fluorescent protein

T-cell surface glycoprotein CD3 epsilon chain

HLA class I histocompatibility antigen, A alpha chain

Beta-2-microglobulin

T-cell surface glycoprotein CD3 zeta chain