SMTL ID : 9j4s.3 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

2 x SER- PRO- ARG- TRP- TYR- PHE- TYR- TYR- LEU: Nucleoprotein(Non-covalent)

SER-PRO-ARG-TRP-TYR-PHE-TYR-TYR-LEU.1: 30 residues within 4Å: Chain E: Y.8, Y.10, E.46, Y.60, R.63, N.64, I.67, Y.68, A.70, Q.71, T.74, E.77, S.78, N.81, L.82, Y.85, L.96, Y.100, D.115, Y.117, Y.124, T.144, K.147, W.148, E.153, R.157, Y.160, E.164, W.168, Y.172 28 PLIP interactions: 28 interactions with chain E Hydrophobic interactions: E:I.67, E:Y.68, E:A.70, E:T.74, E:E.77, E:L.82, E:L.96, E:Y.117, E:Y.124, E:W.148, E:Y.160, E:Y.160 Hydrogen bonds: E:N.64, E:S.78, E:S.78, E:N.81, E:Y.100, E:Y.117, E:T.144, E:K.147, E:R.157, E:Y.160, E:W.168, E:Y.172, E:Y.172 Salt bridges: E:D.115, E:K.147 pi-Cation interactions: E:R.157 SER-PRO-ARG-TRP-TYR-PHE-TYR-TYR-LEU.2: 30 residues within 4Å: Chain G: Y.8, Y.10, E.46, Y.60, R.63, N.64, I.67, Y.68, A.70, Q.71, T.74, E.77, S.78, N.81, Y.85, L.96, Y.100, D.115, Y.117, Y.124, T.144, K.147, W.148, E.153, Q.156, R.157, Y.160, E.164, W.168, Y.172 33 PLIP interactions: 33 interactions with chain G Hydrophobic interactions: G:R.63, G:I.67, G:I.67, G:I.67, G:Y.68, G:A.70, G:Q.71, G:E.77, G:L.96, G:Y.100, G:Y.100, G:Y.124, G:Y.160, G:Y.160 Hydrogen bonds: G:Y.8, G:N.64, G:N.64, G:S.78, G:S.78, G:N.81, G:Y.85, G:Y.100, G:Y.100, G:Y.117, G:Y.117, G:K.147, G:R.157, G:E.164, G:Y.172, G:Y.172 Salt bridges: G:D.115, G:K.147 pi-Cation interactions: G:R.157

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: V.167, H.168, S.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.168, A:S.169, A:S.169 SO4.4: 4 residues within 4Å: Chain B: N.98, N.99, A.100, R.101 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.99, B:A.100, B:R.101 Salt bridges: B:R.101 SO4.5: 5 residues within 4Å: Chain B: K.23, H.76 Chain E: A.137, D.138, T.139 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:A.137, E:T.139 Salt bridges: B:K.23, B:H.76 SO4.6: 4 residues within 4Å: Chain C: G.164, H.208, R.210 Chain E: R.274 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:G.164 Salt bridges: C:H.208, C:R.210, E:R.274 SO4.7: 2 residues within 4Å: Chain E: R.22 Chain F: H.52 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Salt bridges: F:H.52, E:R.22 SO4.8: 4 residues within 4Å: Chain E: D.239 Chain F: R.13, H.14, F.23 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.13, F:H.14 SO4.9: 5 residues within 4Å: Chain F: K.42, E.70, F.71, T.72, Y.79 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.72, F:Y.79 Salt bridges: F:K.42 SO4.11: 8 residues within 4Å: Chain G: S.14, R.15, G.19, P.21, R.76, R.80, R.83, E.90 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:R.15, G:E.90 Salt bridges: G:R.76, G:R.80, G:R.83 SO4.12: 3 residues within 4Å: Chain G: R.22, D.40 Chain H: H.52 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain G Salt bridges: H:H.52, G:R.22 Hydrogen bonds: G:D.40

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: R.19, R.23, N.221 Chain G: S.196, D.197, H.198 7 PLIP interactions: 3 interactions with chain G, 4 interactions with chain A Hydrogen bonds: G:S.196, G:D.197, G:H.198, A:R.19, A:R.19, A:R.23, A:N.221

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

T cell receptor CLA1 beta: AC
T cell receptor CLA1 alpha: BD
HLA class I histocompatibility antigen, B alpha chain: EG
Beta-2-microglobulin: FH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
A

B
I

D
B

E
C

G
F

F
D

H
H

T cell receptor CLA1 beta

T cell receptor CLA1 alpha

HLA class I histocompatibility antigen, B alpha chain

Beta-2-microglobulin

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