SMTL ID : 8qqz.1

Cryo-EM structure of the light-driven sodium pump ErNaR in the pentameric form at pH 8.0

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.63 Å

Oligo State

homo-pentamer

Ligands

46 x LFA: EICOSANE(Non-covalent)(Non-functional Binders)

LFA.1: 7 residues within 4Å: Chain A: F.203, W.206, F.207, A.210, T.211, I.214, S.244 Ligand excluded by PLIP LFA.2: 4 residues within 4Å: Chain A: T.132, I.133, V.136 Ligands: LFA.51 Ligand excluded by PLIP LFA.3: 6 residues within 4Å: Chain A: F.203, F.207, V.243, S.244, V.248 Ligands: LFA.17 Ligand excluded by PLIP LFA.4: 3 residues within 4Å: Chain A: D.229, V.233 Ligands: LFA.8 Ligand excluded by PLIP LFA.5: 5 residues within 4Å: Chain A: L.137, L.140, T.141, V.144 Ligands: LFA.54 Ligand excluded by PLIP LFA.6: 8 residues within 4Å: Chain A: L.33, V.34 Chain B: L.30, V.59, L.63 Chain E: A.37, M.38 Ligands: LFA.37 Ligand excluded by PLIP LFA.7: 2 residues within 4Å: Chain A: L.70 Chain B: L.70 Ligand excluded by PLIP LFA.8: 4 residues within 4Å: Chain A: W.13 Ligands: LFA.4, LFA.14, LFA.18 Ligand excluded by PLIP LFA.9: 9 residues within 4Å: Chain A: V.34, A.37, M.38 Chain B: L.30, L.33 Chain C: L.30, V.59, L.63 Ligands: LFA.37 Ligand excluded by PLIP LFA.10: 7 residues within 4Å: Chain A: M.1, Y.143, Y.147, F.148 Chain E: W.13, V.17 Ligands: LFA.54 Ligand excluded by PLIP LFA.14: 7 residues within 4Å: Chain A: W.13, V.17 Chain B: M.1, Y.143, Y.147, F.148 Ligands: LFA.8 Ligand excluded by PLIP LFA.15: 2 residues within 4Å: Chain B: L.70 Chain C: L.70 Ligand excluded by PLIP LFA.16: 7 residues within 4Å: Chain B: F.203, W.206, F.207, A.210, T.211, I.214, S.244 Ligand excluded by PLIP LFA.17: 5 residues within 4Å: Chain B: R.125, A.129, T.132, I.133 Ligands: LFA.3 Ligand excluded by PLIP LFA.18: 5 residues within 4Å: Chain B: L.137, L.140, T.141, V.144 Ligands: LFA.8 Ligand excluded by PLIP LFA.19: 6 residues within 4Å: Chain B: V.240, V.243, S.244, V.248 Ligands: LMT.24, LFA.28 Ligand excluded by PLIP LFA.20: 3 residues within 4Å: Chain B: D.229, V.233 Ligands: LFA.21 Ligand excluded by PLIP LFA.21: 4 residues within 4Å: Chain B: W.13 Ligands: LFA.20, LFA.25, LFA.29 Ligand excluded by PLIP LFA.22: 8 residues within 4Å: Chain B: V.34, A.37, M.38 Chain C: L.33, V.34 Chain D: L.30, V.59, L.63 Ligand excluded by PLIP LFA.25: 7 residues within 4Å: Chain B: W.13, V.17 Chain C: M.1, Y.143, Y.147, F.148 Ligands: LFA.21 Ligand excluded by PLIP LFA.26: 4 residues within 4Å: Chain C: F.203, W.206, F.207, T.211 Ligand excluded by PLIP LFA.27: 5 residues within 4Å: Chain C: F.24, V.240, V.243, S.244, V.248 Ligand excluded by PLIP LFA.28: 4 residues within 4Å: Chain C: T.132, I.133, V.136 Ligands: LFA.19 Ligand excluded by PLIP LFA.29: 3 residues within 4Å: Chain C: L.140, V.144 Ligands: LFA.21 Ligand excluded by PLIP LFA.30: 4 residues within 4Å: Chain C: W.13, D.229, V.233 Ligands: LFA.32 Ligand excluded by PLIP LFA.31: 2 residues within 4Å: Chain C: L.70 Chain D: L.70 Ligand excluded by PLIP LFA.32: 4 residues within 4Å: Chain C: W.13 Ligands: LFA.30, LFA.38, LFA.43 Ligand excluded by PLIP LFA.35: 8 residues within 4Å: Chain A: L.30, V.59, L.63 Chain D: A.37, M.38 Chain E: L.33 Ligands: LFA.36, LFA.37 Ligand excluded by PLIP LFA.36: 7 residues within 4Å: Chain C: A.37, M.38 Chain D: L.33, V.34 Chain E: L.30, V.59 Ligands: LFA.35 Ligand excluded by PLIP LFA.37: 3 residues within 4Å: Ligands: LFA.6, LFA.9, LFA.35 Ligand excluded by PLIP LFA.38: 7 residues within 4Å: Chain C: W.13, V.17 Chain D: M.1, V.144, Y.147, F.148 Ligands: LFA.32 Ligand excluded by PLIP LFA.39: 2 residues within 4Å: Chain D: L.70 Chain E: L.70 Ligand excluded by PLIP LFA.40: 5 residues within 4Å: Chain D: F.203, W.206, F.207, T.211, I.214 Ligand excluded by PLIP LFA.41: 7 residues within 4Å: Chain D: F.203, F.207, V.240, V.243, S.244, V.248 Ligands: LFA.52 Ligand excluded by PLIP LFA.42: 2 residues within 4Å: Chain D: A.129, T.132 Ligand excluded by PLIP LFA.43: 5 residues within 4Å: Chain D: L.137, L.140, T.141, V.144 Ligands: LFA.32 Ligand excluded by PLIP LFA.44: 4 residues within 4Å: Chain D: D.229, V.232, V.233 Ligands: LFA.45 Ligand excluded by PLIP LFA.45: 4 residues within 4Å: Chain D: W.13 Ligands: LFA.44, LFA.48, LFA.53 Ligand excluded by PLIP LFA.48: 5 residues within 4Å: Chain D: W.13 Chain E: M.1, Y.147, F.148 Ligands: LFA.45 Ligand excluded by PLIP LFA.49: 2 residues within 4Å: Chain A: L.70 Chain E: L.70 Ligand excluded by PLIP LFA.50: 7 residues within 4Å: Chain E: F.203, W.206, F.207, A.210, T.211, I.214, S.244 Ligand excluded by PLIP LFA.51: 5 residues within 4Å: Chain E: V.240, V.243, S.244, V.248 Ligands: LFA.2 Ligand excluded by PLIP LFA.52: 3 residues within 4Å: Chain E: T.132, I.133 Ligands: LFA.41 Ligand excluded by PLIP LFA.53: 3 residues within 4Å: Chain E: L.140, V.144 Ligands: LFA.45 Ligand excluded by PLIP LFA.54: 4 residues within 4Å: Chain E: W.13 Ligands: LFA.5, LFA.10, LFA.55 Ligand excluded by PLIP LFA.55: 4 residues within 4Å: Chain E: W.13, D.229, V.233 Ligands: LFA.54 Ligand excluded by PLIP

10 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.11: 14 residues within 4Å: Chain A: P.45, L.49, V.56, G.121, L.124, W.128 Chain E: V.28, A.31, G.32, Y.35, L.247, V.251, Q.255, A.272 14 PLIP interactions: 9 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:A.31, E:Y.35, E:Y.35, E:L.247, A:W.128 Hydrogen bonds: E:Y.35, E:Y.35, E:Q.255, A:G.121, A:G.121 Water bridges: E:T.39, E:T.39, A:P.45, A:R.48 LMT.12: 14 residues within 4Å: Chain A: A.31, G.32, Y.35, L.247, V.251, Q.255, A.272 Chain B: P.45, L.49, V.56, G.121, L.124, R.125, W.128 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:V.56, B:V.56, B:W.128, A:Y.35, A:L.247 Hydrogen bonds: B:P.45, B:G.121, B:G.121, A:Y.35, A:Y.35, A:Q.255 Water bridges: B:R.48, A:T.39, A:T.39 LMT.13: 9 residues within 4Å: Chain A: F.24, S.199, R.200, F.203, L.247, V.251, I.252, Q.255 Chain B: W.128 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.24, A:V.251, B:W.128 Hydrogen bonds: A:S.199, A:R.200, A:Q.255 Salt bridges: B:R.125 LMT.23: 16 residues within 4Å: Chain B: V.28, A.31, G.32, Y.35, L.247, V.251, Q.255, A.272 Chain C: P.45, L.49, V.56, G.121, L.124, R.125, W.128 Ligands: LMT.24 15 PLIP interactions: 6 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:V.56, C:W.128, B:A.31, B:Y.35, B:Y.35, B:L.247 Hydrogen bonds: C:P.45, C:G.121, C:G.121, B:Y.35, B:Y.35, B:Q.255 Water bridges: C:R.48, B:T.39, B:T.39 LMT.24: 13 residues within 4Å: Chain B: F.24, S.199, R.200, F.203, V.243, L.247, V.251, I.252, Q.255 Chain C: L.103, W.128 Ligands: LFA.19, LMT.23 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.24, B:V.243, B:V.251, C:W.128, C:W.128 Hydrogen bonds: B:S.199, B:R.200, B:R.200, B:Q.255 LMT.33: 16 residues within 4Å: Chain C: V.28, A.31, G.32, Y.35, L.247, V.251, Q.255, A.272 Chain D: P.45, L.49, V.56, G.121, L.124, R.125, W.128 Ligands: LMT.34 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:A.31, C:Y.35, C:Y.35, C:L.247, D:V.56, D:W.128 Hydrogen bonds: C:Y.35, C:Y.35, C:Q.255, D:P.45, D:G.121 Water bridges: C:T.39, C:T.39, D:R.48 LMT.34: 12 residues within 4Å: Chain C: F.24, S.199, R.200, F.203, V.243, L.247, V.251, I.252, Q.255 Chain D: R.125, W.128 Ligands: LMT.33 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.24, C:V.243, C:L.247, C:V.251, D:W.128 Hydrogen bonds: C:S.199, C:R.200, C:Q.255 Salt bridges: D:R.125 LMT.46: 15 residues within 4Å: Chain D: A.31, G.32, Y.35, L.247, V.251, Q.255, A.272 Chain E: P.45, L.49, V.56, M.108, G.121, L.124, W.128 Ligands: LMT.47 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:Y.35, D:L.247, E:V.56, E:W.128 Hydrogen bonds: D:Y.35, D:Y.35, D:Q.255, E:P.45, E:G.121, E:G.121 Water bridges: E:R.48 LMT.47: 11 residues within 4Å: Chain D: F.24, S.199, R.200, F.203, L.247, V.248, V.251, I.252, Q.255 Chain E: W.128 Ligands: LMT.46 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:F.24, D:L.247, D:V.248, D:V.251, E:W.128, E:W.128 Hydrogen bonds: D:S.199, D:R.200, D:Q.255 LMT.56: 10 residues within 4Å: Chain A: R.125, W.128 Chain E: F.24, S.199, R.200, F.203, L.247, V.251, I.252, Q.255 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:F.24, E:L.247, E:V.251, A:W.128, A:W.128 Hydrogen bonds: E:S.199, E:R.200, E:Q.255 Salt bridges: A:R.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Podoliak, E. et al., A subgroup of light-driven sodium pumps with an additional Schiff base counterion. Nat Commun (2024)

Release Date

2024-04-24

Peptides

Bacteriorhodopsin-like protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Bacteriorhodopsin-like protein

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