SMTL ID : 8xma.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.370, H.387, E.420, C.433 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.370, A:H.387, A:E.420, A:C.433 ZN.2: 4 residues within 4Å: Chain A: H.408, I.412, H.413 Chain B: C.437 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.437, A:H.408, A:H.413 ZN.3: 4 residues within 4Å: Chain A: E.371, H.373, C.446, C.447 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.371, A:H.373, A:C.446, A:C.446, A:C.447 ZN.4: 3 residues within 4Å: Chain A: D.47, H.251, D.255 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.47, A:D.47, A:H.251, A:D.255, A:D.255 ZN.9: 4 residues within 4Å: Chain B: H.370, H.387, E.420, C.433 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.370, B:H.387, B:E.420, B:C.433 ZN.10: 4 residues within 4Å: Chain A: C.437 Chain B: H.408, I.412, 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.11: 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 ZN.12: 3 residues within 4Å: Chain B: D.47, H.251, D.255 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.47, B:D.47, B:H.251, B:D.255, B:D.255

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

AV0.5: 11 residues within 4Å: Chain A: V.53, F.60, K.69, W.74, A.77, M.80, V.84 Chain B: L.336, K.337, A.340 Ligands: Y01.6 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.53, A:F.60, A:F.60, A:W.74, A:W.74, A:A.77, A:V.84, B:L.336, B:A.340 AV0.13: 9 residues within 4Å: Chain A: Y.333, K.337, A.340 Chain B: V.53, F.60, R.63, A.77, M.80 Ligands: Y01.8 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.53, B:F.60, B:F.60, B:A.77, A:K.337, A:A.340 Hydrogen bonds: B:R.63 Salt bridges: B:R.63

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 9 residues within 4Å: Chain A: L.49, V.53, V.56, F.60, V.84, F.88 Chain B: Y.333, L.336 Ligands: AV0.5 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.49, A:L.49, A:V.53, A:V.56, A:F.60, A:V.84, A:F.88, B:Y.333, B:L.336 Y01.7: 6 residues within 4Å: Chain A: L.97, V.322, C.326, L.329, Y.330, Y.333 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.97, A:V.322, A:L.329, A:Y.330, A:Y.333 Y01.8: 8 residues within 4Å: Chain A: I.87, Y.333 Chain B: V.53, V.56, F.60, V.84, F.88 Ligands: AV0.13 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.87, B:V.53, B:V.56, B:F.60, B:V.84, B:F.88 Y01.14: 5 residues within 4Å: Chain B: I.101, C.326, L.329, Y.330, Y.333 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.101, B:L.329, B:Y.330

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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