SMTL ID : 9j4u.1

Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x LEU- LEU- LEU- ASP- ARG- LEU- ASN- GLN- LEU: Nucleoprotein(Non-covalent)

LEU-LEU-LEU-ASP-ARG-LEU-ASN-GLN-LEU.1: 40 residues within 4Å: Chain A: M.6, Y.8, F.10, M.46, Y.60, E.64, K.67, V.68, A.70, H.71, T.74, V.77, D.78, T.81, L.82, Y.85, R.98, Y.100, Y.117, Y.124, T.144, K.147, W.148, V.153, Q.156, L.157, A.159, Y.160, T.164, W.168, Y.172 Chain C: A.30, Q.32, S.33, Y.52, G.95 Chain D: E.97, L.98, N.99, Y.101 53 PLIP interactions: 37 interactions with chain A, 6 interactions with chain C, 10 interactions with chain D Hydrophobic interactions: A:Y.8, A:F.10, A:Y.60, A:K.67, A:V.68, A:A.70, A:D.78, A:L.82, A:L.82, A:Y.100, A:Y.117, A:Y.117, A:Y.124, A:T.144, A:W.148, A:L.157, A:Y.160, A:Y.160, A:T.164, A:W.168, A:W.168, C:A.30, D:Y.101 Hydrogen bonds: A:E.64, A:K.67, A:D.78, A:Y.100, A:Y.117, A:T.144, A:Q.156, A:Q.156, A:Y.160, A:Y.172, A:Y.172, C:Q.32, C:Q.32, C:S.33, D:Y.51, D:E.97, D:L.98 Water bridges: A:R.98, A:R.98, A:R.98, A:Y.100, C:S.33, C:A.94, D:E.97, D:E.97, D:E.97, D:E.97, D:N.99, D:E.102 Salt bridges: A:K.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, P. et al., Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors. To Be Published

Release Date

2025-08-13

Peptides

MHC class I antigen: A
Beta-2-microglobulin: B
LLL epitope specific TCR APHLA: C
LLL epitope specific TCR BETA: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

MHC class I antigen

Beta-2-microglobulin

LLL epitope specific TCR APHLA

LLL epitope specific TCR BETA

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