SMTL ID : 8do1.1

Cryo-EM structure of the human Sec61 complex inhibited by ipomoeassin F

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x SXF: [(1~{S},3~{R},4~{S},5~{R},6~{R},8~{R},10~{S},23~{R},24~{R},25~{R},26~{R})-5-acetyloxy-6-methyl-4,26-bis(oxidanyl)-17,20-bis(oxidanylidene)-10-pentyl-24-[(~{E})-3-phenylprop-2-enoyl]oxy-2,7,9,21,27-pentaoxatricyclo[21.3.1.0^{3,8}]heptacosan-25-yl] (~{E})-2-methylbut-2-enoate(Non-covalent)

SXF.1: 25 residues within 4Å: Chain A: F.62, M.65, I.68, L.69, I.81, S.82, V.85, T.86, G.88, L.89, Q.92, I.123, G.126, Q.127, V.130, Y.131, I.183, I.289, I.292, L.293, A.296, L.297, N.300, W.379, L.449 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:F.62, A:F.62, A:I.68, A:L.69, A:L.69, A:I.81, A:V.85, A:T.86, A:L.89, A:L.89, A:I.123, A:I.123, A:Q.127, A:Y.131, A:I.183, A:I.289, A:I.292, A:I.292, A:I.292, A:A.296, A:W.379 Hydrogen bonds: A:S.82, A:S.82, A:Q.127, A:N.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Itskanov, S. et al., A common mechanism of Sec61 translocon inhibition by small molecules. Nat.Chem.Biol. (2023)

Release Date

2023-05-24

Peptides

Protein transport protein Sec61 subunit alpha isoform 1: A
Protein transport protein Sec61 subunit gamma: B
Protein transport protein Sec61 subunit beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Protein transport protein Sec61 subunit alpha isoform 1

Protein transport protein Sec61 subunit gamma

Protein transport protein Sec61 subunit beta

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