SMTL ID : 8hsi.1

Cryo-EM structure of human TMEM87A, PE-bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.79, T.81, L.124 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.62 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: Q.126, N.127 No protein-ligand interaction detected (PLIP)

1 x L9Q: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

L9Q.4: 22 residues within 4Å: Chain A: I.258, I.262, A.308, R.309, L.311, V.312, V.315, Y.340, E.347, D.371, T.372, C.375, W.376, F.379, L.408, V.412, S.415, W.445, F.449, I.452, L.453, I.456 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.315, A:W.376, A:L.408, A:I.452, A:I.456 Hydrogen bonds: A:D.371, A:S.415 Salt bridges: A:R.305, A:R.309, A:R.309

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 13 residues within 4Å: Chain A: R.257, I.258, W.261, L.307, T.310, L.311, I.314, Y.319, R.325, L.330, V.334, V.335, A.338 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.258, A:L.311, A:I.314, A:I.314, A:Y.319, A:Y.319, A:A.338 CLR.6: 9 residues within 4Å: Chain A: P.225, I.228, F.229, V.232, M.233, V.236, W.439, L.447, S.450 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.225, A:F.229, A:V.232, A:W.439, A:W.439, A:L.447

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, H. et al., GolpHCat (TMEM87A), a unique voltage-dependent cation channel in Golgi apparatus, contributes to Golgi-pH maintenance and hippocampus-dependent memory. Nat Commun (2024)

Release Date

2023-12-27

Peptides

Transmembrane protein 87A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Transmembrane protein 87A