SMTL ID : 9ctu.1

Cryo-EM structure of SARS-CoV-2 M (short conformation)bound to C1P

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

2 x 1PX: (2S,3R,4E)-2-(hexadecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate(Non-covalent)

1PX.1: 10 residues within 4Å: Chain E: R.44, F.45, I.48, I.52, W.55, M.109, W.110, F.112, T.130, R.131 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:F.45, E:I.48, E:I.48, E:I.52, E:W.55, E:W.55, E:W.110 Hydrogen bonds: E:R.44, E:W.110, E:T.130 Salt bridges: E:R.131 1PX.3: 12 residues within 4Å: Chain F: R.44, F.45, I.48, L.51, I.52, W.55, M.109, W.110, F.112, I.128, T.130, R.131 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:F.45, F:I.48, F:L.51, F:I.52, F:W.55, F:W.55, F:W.55, F:W.110 Hydrogen bonds: F:R.44, F:W.110, F:T.130, F:T.130, F:T.130 Salt bridges: F:R.131

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain E: Y.95, S.99, S.111, N.113, T.116, N.117 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:S.99, E:S.111, E:N.113, E:T.116 K.4: 6 residues within 4Å: Chain F: Y.95, S.99, S.111, N.113, T.116, N.117 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:S.99, F:S.111, F:N.113, F:T.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dutta, M. et al., Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly. To Be Published

Release Date

2024-11-06

Peptides

short conformation Fab light chain: AC
short conformation Fab heavy chain: BD
Membrane protein: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
E

B
D

D
F

E
A

F
B

Membrane

We predict this structure to be a membrane protein.
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short conformation Fab light chain

short conformation Fab heavy chain

Membrane protein

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