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SMTL ID : 9rup.1

Cryo-EM structure of TCRpub/pMHC dimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.11 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

2 x PHE- THR- SER- ASP- TYR- TYR- GLN- LEU- TYR: ORF3a_207-215 epitope(Non-covalent)

PHE-THR-SER-ASP-TYR-TYR-GLN-LEU-TYR.1:

25 residues within 4Å:

Chain A: F.45, G.58, Y.60
Chain D: Y.5, Y.57, E.61, T.62, N.64, M.65, H.68, N.75, T.78, L.79, I.93, I.95, Y.97, R.112, D.114, T.141, W.145, Q.153, Y.157, R.161, G.165, Y.169

22 PLIP interactions:

19 interactions with chain D, 3 interactions with chain A

Hydrophobic interactions: D:Y.5, D:E.61, D:H.68, D:N.75, D:L.79, D:I.93, D:W.145, D:Q.153, A:F.45, A:Y.60
Hydrogen bonds: D:Y.5, D:Y.57, D:Y.57, D:N.75, D:R.112, D:R.112, D:D.114, D:D.114, D:Y.169, D:Y.169, A:Y.60
pi-Stacking: D:Y.57

PHE-THR-SER-ASP-TYR-TYR-GLN-LEU-TYR.2:

29 residues within 4Å:

Chain E: F.45, K.48, G.58, S.59, Y.60
Chain F: E.100
Chain H: M.3, Y.5, Y.57, E.61, T.62, N.64, M.65, H.68, N.75, T.78, I.93, I.95, Y.97, D.114, T.141, K.144, W.145, Q.153, R.154, Y.157, R.161, G.165, Y.169

19 PLIP interactions:

17 interactions with chain H, 2 interactions with chain E

Hydrophobic interactions: H:Y.5, H:Y.57, H:N.64, H:H.68, H:I.93, H:Q.153, E:F.45, E:Y.60
Hydrogen bonds: H:Y.5, H:T.62, H:N.75, H:D.114, H:W.145, H:R.154, H:R.154, H:Y.157, H:Y.169
Salt bridges: H:K.144, H:R.161

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Akil, C. et al., Cryo-EM structure of TCRpub/pMHC dimer. To Be Published

Release Date

2025-08-13

Peptides

T cell receptor, alpha chain: AE
T cell receptor, beta chain: BF
Beta-2-microglobulin: CG
MHC class I antigen: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
a

B
B

F
b

C
E

G
e

D
C

H
c

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

T cell receptor, alpha chain

T cell receptor, beta chain

Beta-2-microglobulin

Toggle Identical (CG)

MHC class I antigen

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