SMTL ID : 7jlp.1

cryo-EM structure of human ATG9A in nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

45 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)(Non-functional Binders)

POV.1: 10 residues within 4Å: Chain A: E.69, I.138, F.142, R.146, Y.249, L.253, A.296, N.297, L.300 Ligands: POV.2 Ligand excluded by PLIP POV.2: 8 residues within 4Å: Chain A: T.80, L.132, A.139, F.142, L.303, W.307, L.310 Ligands: POV.1 Ligand excluded by PLIP POV.3: 10 residues within 4Å: Chain A: L.320, L.327, N.366, L.373, S.423, F.424, P.426, Y.471, A.473 Ligands: POV.4 Ligand excluded by PLIP POV.4: 11 residues within 4Å: Chain A: V.241, A.312, L.320, R.330, A.466, Q.467, Y.471, A.473, V.474, I.476 Ligands: POV.3 Ligand excluded by PLIP POV.5: 6 residues within 4Å: Chain A: F.232, L.234, F.242, V.485, I.489, C.493 Ligand excluded by PLIP POV.6: 6 residues within 4Å: Chain A: Y.89, A.317 Chain C: A.393, Y.397 Ligands: POV.7, POV.8 Ligand excluded by PLIP POV.7: 2 residues within 4Å: Ligands: POV.6, POV.8 Ligand excluded by PLIP POV.8: 5 residues within 4Å: Chain A: V.84, Y.89 Chain C: A.393 Ligands: POV.6, POV.7 Ligand excluded by PLIP POV.9: 6 residues within 4Å: Chain A: T.60, L.63, I.67, F.68, W.158 Ligands: POV.31 Ligand excluded by PLIP POV.10: 3 residues within 4Å: Chain A: L.63, I.67, W.158 Ligand excluded by PLIP POV.11: 9 residues within 4Å: Chain A: L.83, L.112, P.113 Chain C: I.387, L.391, H.406, T.410 Ligands: POV.13, POV.32 Ligand excluded by PLIP POV.12: 5 residues within 4Å: Chain A: S.370, P.371, L.372, L.373, L.376 Ligand excluded by PLIP POV.13: 8 residues within 4Å: Chain A: A.78, F.79, F.82, P.113, D.114, F.116, P.118 Ligands: POV.11 Ligand excluded by PLIP POV.14: 2 residues within 4Å: Chain A: L.372 Ligands: POV.24 Ligand excluded by PLIP POV.15: 5 residues within 4Å: Chain A: H.406, T.410, L.413, T.417 Ligands: POV.26 Ligand excluded by PLIP POV.16: 10 residues within 4Å: Chain B: E.69, I.138, F.142, R.146, Y.249, L.253, A.296, N.297, L.300 Ligands: POV.17 Ligand excluded by PLIP POV.17: 8 residues within 4Å: Chain B: T.80, L.132, A.139, F.142, L.303, W.307, L.310 Ligands: POV.16 Ligand excluded by PLIP POV.18: 10 residues within 4Å: Chain B: L.320, L.327, N.366, L.373, S.423, F.424, P.426, Y.471, A.473 Ligands: POV.19 Ligand excluded by PLIP POV.19: 11 residues within 4Å: Chain B: V.241, A.312, L.320, R.330, A.466, Q.467, Y.471, A.473, V.474, I.476 Ligands: POV.18 Ligand excluded by PLIP POV.20: 6 residues within 4Å: Chain B: F.232, L.234, F.242, V.485, I.489, C.493 Ligand excluded by PLIP POV.21: 6 residues within 4Å: Chain A: A.393, Y.397 Chain B: Y.89, A.317 Ligands: POV.22, POV.23 Ligand excluded by PLIP POV.22: 2 residues within 4Å: Ligands: POV.21, POV.23 Ligand excluded by PLIP POV.23: 5 residues within 4Å: Chain A: A.393 Chain B: V.84, Y.89 Ligands: POV.21, POV.22 Ligand excluded by PLIP POV.24: 6 residues within 4Å: Chain B: T.60, L.63, I.67, F.68, W.158 Ligands: POV.14 Ligand excluded by PLIP POV.25: 3 residues within 4Å: Chain B: L.63, I.67, W.158 Ligand excluded by PLIP POV.26: 9 residues within 4Å: Chain A: I.387, L.391, H.406, T.410 Chain B: L.83, L.112, P.113 Ligands: POV.15, POV.28 Ligand excluded by PLIP POV.27: 5 residues within 4Å: Chain B: S.370, P.371, L.372, L.373, L.376 Ligand excluded by PLIP POV.28: 8 residues within 4Å: Chain B: A.78, F.79, F.82, P.113, D.114, F.116, P.118 Ligands: POV.26 Ligand excluded by PLIP POV.29: 1 residues within 4Å: Ligands: POV.41 Ligand excluded by PLIP POV.30: 5 residues within 4Å: Chain B: H.406, T.410, L.413, T.417 Ligands: POV.43 Ligand excluded by PLIP POV.31: 2 residues within 4Å: Chain C: L.372 Ligands: POV.9 Ligand excluded by PLIP POV.32: 5 residues within 4Å: Chain C: H.406, T.410, L.413, T.417 Ligands: POV.11 Ligand excluded by PLIP POV.33: 10 residues within 4Å: Chain C: E.69, I.138, F.142, R.146, Y.249, L.253, A.296, N.297, L.300 Ligands: POV.34 Ligand excluded by PLIP POV.34: 8 residues within 4Å: Chain C: T.80, L.132, A.139, F.142, L.303, W.307, L.310 Ligands: POV.33 Ligand excluded by PLIP POV.35: 10 residues within 4Å: Chain C: L.320, L.327, N.366, L.373, S.423, F.424, P.426, Y.471, A.473 Ligands: POV.36 Ligand excluded by PLIP POV.36: 11 residues within 4Å: Chain C: V.241, A.312, L.320, R.330, A.466, Q.467, Y.471, A.473, V.474, I.476 Ligands: POV.35 Ligand excluded by PLIP POV.37: 6 residues within 4Å: Chain C: F.232, L.234, F.242, V.485, I.489, C.493 Ligand excluded by PLIP POV.38: 6 residues within 4Å: Chain B: A.393, Y.397 Chain C: Y.89, A.317 Ligands: POV.39, POV.40 Ligand excluded by PLIP POV.39: 2 residues within 4Å: Ligands: POV.38, POV.40 Ligand excluded by PLIP POV.40: 5 residues within 4Å: Chain B: A.393 Chain C: V.84, Y.89 Ligands: POV.38, POV.39 Ligand excluded by PLIP POV.41: 6 residues within 4Å: Chain C: T.60, L.63, I.67, F.68, W.158 Ligands: POV.29 Ligand excluded by PLIP POV.42: 3 residues within 4Å: Chain C: L.63, I.67, W.158 Ligand excluded by PLIP POV.43: 9 residues within 4Å: Chain B: I.387, L.391, H.406, T.410 Chain C: L.83, L.112, P.113 Ligands: POV.30, POV.45 Ligand excluded by PLIP POV.44: 5 residues within 4Å: Chain C: S.370, P.371, L.372, L.373, L.376 Ligand excluded by PLIP POV.45: 8 residues within 4Å: Chain C: A.78, F.79, F.82, P.113, D.114, F.116, P.118 Ligands: POV.43 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maeda, S. et al., Structure, lipid scrambling activity and role in autophagosome formation of ATG9A. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-10-28

Peptides

Autophagy-related protein 9A: ABC

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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Autophagy-related protein 9A

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