SMTL ID : 8xm6.1

Cryo-EM structure of human ZnT1 WT, in the absence of zinc, determined in an outward-facing conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.370, H.387, E.420, C.433 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.370, A:H.387, A:E.420, A:E.420, A:C.433 ZN.2: 3 residues within 4Å: Chain A: H.408, H.413 Chain B: C.437 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.408, A:H.413, B:C.437 ZN.3: 4 residues within 4Å: Chain A: E.371, H.373, C.446, C.447 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.371, A:H.373, A:C.446, A:C.447 ZN.8: 4 residues within 4Å: Chain B: H.370, H.387, E.420, C.433 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.370, B:H.387, B:E.420, B:E.420, B:C.433 ZN.9: 3 residues within 4Å: Chain A: C.437 Chain B: H.408, H.413 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.408, B:H.413, A:C.437 ZN.10: 4 residues within 4Å: Chain B: E.371, H.373, C.446, C.447 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.371, B:H.373, B:C.446, B:C.447

2 x AV0: Lauryl Maltose Neopentyl Glycol(Non-covalent)

AV0.4: 11 residues within 4Å: Chain A: V.53, V.56, F.60, R.63, K.69, W.74 Chain B: Y.333, L.336, A.340, L.344 Ligands: Y01.5 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.53, A:V.56, A:F.60, A:F.60, A:W.74, B:L.336, B:L.344 Hydrogen bonds: A:R.63, A:W.74 Salt bridges: A:R.63 AV0.11: 13 residues within 4Å: Chain A: L.336, K.337, A.340, L.341 Chain B: V.53, F.60, R.63, K.69, W.74, M.80, G.81 Ligands: Y01.7, Y01.13 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.53, B:F.60, B:F.60, B:W.74, A:L.336, A:K.337, A:A.340, A:L.341 Salt bridges: B:K.69

5 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.5: 9 residues within 4Å: Chain A: L.49, V.53, F.60, V.84, F.88 Chain B: T.90, Y.333, L.336 Ligands: AV0.4 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.90, B:Y.333, B:L.336, A:L.49, A:F.60 Y01.6: 5 residues within 4Å: Chain A: C.326, L.329, Y.330, Y.333 Ligands: Y01.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.329, A:Y.330, A:Y.330, A:Y.333, A:Y.333 Hydrogen bonds: A:Y.330 Y01.7: 6 residues within 4Å: Chain A: F.94, L.329, Y.333 Ligands: Y01.6, AV0.11, Y01.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.94, A:L.329 Y01.12: 6 residues within 4Å: Chain B: F.94, L.97, C.326, L.329, Y.330, Y.333 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.94, B:Y.330, B:Y.333, B:Y.333 Salt bridges: B:K.337 Y01.13: 10 residues within 4Å: Chain A: T.90, Y.333 Chain B: L.49, V.53, V.56, F.60, V.84, F.88 Ligands: Y01.7, AV0.11 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.49, B:V.56, B:F.60, B:V.84, B:F.88, A:T.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Long, Y. et al., Structural insights into human zinc transporter ZnT1 mediated Zn 2+ efflux. Embo Rep. (2024)

Release Date

2024-10-30

Peptides

Proton-coupled zinc antiporter SLC30A1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Membrane

We predict this structure to be a membrane protein.
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Proton-coupled zinc antiporter SLC30A1

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