SMTL ID : 7d0i.1

Cryo-EM structure of Schizosaccharomyces pombe Atg9

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x LMN: Lauryl Maltose Neopentyl Glycol(Non-covalent)

LMN.1: 14 residues within 4Å: Chain A: F.264, D.347, E.376, W.377, N.378, N.380, N.422, F.425, V.429, W.463, R.466, Q.472, D.476 Ligands: LMN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.264, A:W.377, A:W.377, A:F.425 Hydrogen bonds: A:E.376, A:E.376, A:R.466, A:R.466, A:Q.472 LMN.2: 15 residues within 4Å: Chain A: T.195, Q.209, V.213, F.261, L.268, Y.271, H.373, W.377, Y.432, L.433, N.437, R.440, L.607, E.610 Ligands: LMN.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.213, A:V.213, A:F.261, A:L.268, A:Y.271, A:Y.271, A:W.377, A:Y.432, A:Y.432 Hydrogen bonds: A:T.195, A:T.195, A:Q.209, A:H.373, A:N.437, A:R.440 Salt bridges: A:H.373 LMN.3: 15 residues within 4Å: Chain B: F.264, D.347, E.376, W.377, N.378, N.380, W.381, N.422, F.425, V.429, W.463, R.466, Q.472, D.476 Ligands: LMN.4 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.264, B:W.377, B:W.377, B:W.377, B:W.377, B:W.381, B:F.425 Hydrogen bonds: B:E.376, B:E.376, B:N.380, B:R.466, B:R.466, B:Q.472 LMN.4: 14 residues within 4Å: Chain B: T.195, Q.209, F.261, L.268, Y.271, H.373, W.377, Y.432, L.433, N.437, R.440, L.607, E.610 Ligands: LMN.3 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.261, B:L.268, B:Y.271, B:Y.271, B:W.377, B:Y.432, B:Y.432 Hydrogen bonds: B:T.195, B:T.195, B:Q.209, B:H.373, B:N.437, B:R.440 Salt bridges: B:H.373, B:H.373 LMN.5: 14 residues within 4Å: Chain C: F.264, D.347, E.376, W.377, N.378, N.380, W.381, F.425, V.429, W.463, R.466, Q.472, D.476 Ligands: LMN.6 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.264, C:W.377, C:W.377, C:W.377, C:W.381, C:F.425 Hydrogen bonds: C:N.380, C:R.466, C:R.466, C:Q.472, C:Q.472 LMN.6: 14 residues within 4Å: Chain C: T.195, G.196, Q.209, V.213, F.261, L.268, Y.271, H.373, W.377, Y.432, R.440, L.607, E.610 Ligands: LMN.5 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.213, C:F.261, C:L.268, C:Y.271, C:Y.271, C:W.377, C:Y.432, C:Y.432 Hydrogen bonds: C:T.195, C:T.195, C:Q.209, C:R.440 Salt bridges: C:H.373 LMN.7: 15 residues within 4Å: Chain D: F.264, D.347, E.376, W.377, N.378, N.380, W.381, N.422, F.425, V.429, W.463, R.466, Q.472, D.476 Ligands: LMN.8 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.264, D:F.264, D:W.377, D:W.377, D:W.377, D:W.377, D:W.381, D:F.425 Hydrogen bonds: D:E.376, D:E.376, D:N.380, D:R.466, D:R.466, D:Q.472 LMN.8: 14 residues within 4Å: Chain D: T.195, Q.209, F.261, L.268, Y.271, H.373, W.377, Y.432, L.433, N.437, R.440, L.607, E.610 Ligands: LMN.7 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:F.261, D:L.268, D:Y.271, D:W.377, D:Y.432, D:Y.432 Hydrogen bonds: D:T.195, D:T.195, D:T.195, D:Q.209, D:H.373, D:N.437, D:R.440, D:E.610 Salt bridges: D:H.373, D:H.373 LMN.9: 14 residues within 4Å: Chain E: F.264, D.347, E.376, W.377, N.378, N.380, W.381, F.425, V.429, W.463, R.466, Q.472, D.476 Ligands: LMN.10 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:F.264, E:W.377, E:W.377, E:W.381, E:F.425, E:F.425 Hydrogen bonds: E:E.376, E:N.380, E:R.466, E:R.466, E:Q.472 LMN.10: 14 residues within 4Å: Chain E: T.195, Q.209, F.261, F.264, L.268, Y.271, H.373, W.377, Y.432, L.433, N.437, L.607, E.610 Ligands: LMN.9 19 PLIP interactions: 19 interactions with chain E Hydrophobic interactions: E:F.261, E:F.264, E:L.268, E:Y.271, E:Y.271, E:Y.271, E:W.377, E:Y.432, E:Y.432 Hydrogen bonds: E:T.195, E:T.195, E:T.195, E:Q.209, E:H.373, E:N.437, E:R.440, E:E.610 Salt bridges: E:H.373, E:H.373 LMN.11: 14 residues within 4Å: Chain F: F.264, D.347, E.376, W.377, N.378, N.380, N.422, F.425, V.429, W.463, R.466, Q.472, D.476 Ligands: LMN.12 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:F.264, F:F.264, F:W.377, F:W.377, F:W.377, F:W.377, F:F.425 Hydrogen bonds: F:E.376, F:E.376, F:R.466, F:R.466, F:Q.472 LMN.12: 15 residues within 4Å: Chain F: T.195, Q.209, V.213, F.261, L.268, Y.271, H.373, W.377, Y.432, L.433, N.437, R.440, L.607, E.610 Ligands: LMN.11 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:V.213, F:F.261, F:L.268, F:Y.271, F:W.377, F:Y.432, F:Y.432 Hydrogen bonds: F:T.195, F:T.195, F:T.195, F:Q.209, F:H.373, F:R.440, F:E.610 Salt bridges: F:H.373, F:H.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matoba, K. et al., Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-10-28

Peptides

Autophagy-related protein 9: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
F

D
H

E
J

F
L

Membrane

We predict this structure to be a membrane protein.
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Autophagy-related protein 9