SMTL ID : 7lft.1

Cryo-EM structure of human Apo CNGA1 channel in K+/Ca2+

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 12 residues within 4Å: Chain A: T.51, M.52, A.55, L.62, Y.66, V.178, H.182, L.215, A.216, Y.219 Ligands: CLR.2, CPL.18 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.55, A:Y.66, A:V.178, A:H.182, A:Y.219, A:Y.219, A:Y.219 CLR.2: 10 residues within 4Å: Chain A: L.44, M.47, Y.48, T.51, M.52, Y.66, Y.69, W.70, L.73 Ligands: CLR.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:M.47, A:Y.48, A:Y.66, A:Y.69, A:W.70, A:W.70, A:L.73 CLR.12: 12 residues within 4Å: Chain B: T.51, M.52, A.55, L.62, Y.66, V.178, H.182, L.215, A.216, Y.219 Ligands: CLR.13, CPL.26 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.55, B:Y.66, B:V.178, B:H.182, B:Y.219, B:Y.219, B:Y.219 CLR.13: 10 residues within 4Å: Chain B: L.44, M.47, Y.48, T.51, M.52, Y.66, Y.69, W.70, L.73 Ligands: CLR.12 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:M.47, B:Y.48, B:Y.66, B:Y.69, B:W.70, B:W.70, B:L.73 CLR.20: 12 residues within 4Å: Chain C: T.51, M.52, A.55, L.62, Y.66, V.178, H.182, L.215, A.216, Y.219 Ligands: CLR.21, CPL.34 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.55, C:Y.66, C:V.178, C:H.182, C:Y.219, C:Y.219, C:Y.219 CLR.21: 10 residues within 4Å: Chain C: L.44, M.47, Y.48, T.51, M.52, Y.66, Y.69, W.70, L.73 Ligands: CLR.20 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:M.47, C:Y.48, C:Y.66, C:Y.69, C:W.70, C:W.70, C:L.73 CLR.28: 12 residues within 4Å: Chain D: T.51, M.52, A.55, L.62, Y.66, V.178, H.182, L.215, A.216, Y.219 Ligands: CPL.7, CLR.29 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.55, D:Y.66, D:V.178, D:H.182, D:Y.219, D:Y.219, D:Y.219 CLR.29: 10 residues within 4Å: Chain D: L.44, M.47, Y.48, T.51, M.52, Y.66, Y.69, W.70, L.73 Ligands: CLR.28 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:M.47, D:Y.48, D:Y.66, D:Y.69, D:W.70, D:W.70, D:L.73

24 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

CPL.3: 7 residues within 4Å: Chain A: F.152, Q.156, Y.176, I.177, I.180, I.258, T.261 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.152, A:Y.176, A:Y.176, A:I.180, A:I.258, A:T.261 CPL.4: 6 residues within 4Å: Chain A: V.187, S.190, I.191, A.194 Ligands: CPL.5, CPL.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.187 CPL.5: 10 residues within 4Å: Chain A: I.191, A.194, I.195, R.241, S.243, V.246, F.247, V.250 Ligands: CPL.4, CPL.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.191, A:V.246, A:F.247 CPL.6: 14 residues within 4Å: Chain A: I.54, A.57, C.58, D.60, N.136, Y.137, E.139, L.142, W.183, V.187, S.190, K.193 Ligands: CPL.4, CPL.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.54, A:Y.137, A:E.139, A:L.142, A:W.183 Hydrogen bonds: A:S.190 Salt bridges: A:K.193 CPL.7: 20 residues within 4Å: Chain A: R.241, D.242, S.243, V.246, V.249, V.250, L.253, I.254, L.257 Chain D: V.174, V.178, E.211, R.214, A.216, R.217, Y.219, V.220, L.223 Ligands: CPL.5, CLR.28 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:R.241, A:D.242, A:V.246, A:V.250, A:L.253, A:L.257, D:V.174, D:V.178, D:Y.219, D:Y.219, D:L.223 Hydrogen bonds: A:D.242, A:S.243, A:S.243, A:S.243 Salt bridges: A:R.241 CPL.8: 7 residues within 4Å: Chain A: L.133, Y.137, E.139, L.142, N.143, L.146 Ligands: CPL.6 No protein-ligand interaction detected (PLIP) CPL.14: 7 residues within 4Å: Chain B: F.152, Q.156, Y.176, I.177, I.180, I.258, T.261 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.152, B:Y.176, B:Y.176, B:I.180, B:I.258, B:T.261 CPL.15: 6 residues within 4Å: Chain B: V.187, S.190, I.191, A.194 Ligands: CPL.16, CPL.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.187 CPL.16: 10 residues within 4Å: Chain B: I.191, A.194, I.195, R.241, S.243, V.246, F.247, V.250 Ligands: CPL.15, CPL.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.191, B:V.246, B:F.247 CPL.17: 14 residues within 4Å: Chain B: I.54, A.57, C.58, D.60, N.136, Y.137, E.139, L.142, W.183, V.187, S.190, K.193 Ligands: CPL.15, CPL.19 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.54, B:Y.137, B:E.139, B:L.142, B:W.183 Hydrogen bonds: B:S.190 Salt bridges: B:K.193 CPL.18: 20 residues within 4Å: Chain A: V.174, V.178, E.211, R.214, A.216, R.217, Y.219, V.220, L.223 Chain B: R.241, D.242, S.243, V.246, V.249, V.250, L.253, I.254, L.257 Ligands: CLR.1, CPL.16 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:R.241, B:D.242, B:V.246, B:V.250, B:L.253, B:L.257, A:V.174, A:V.178, A:Y.219, A:Y.219, A:L.223 Hydrogen bonds: B:D.242, B:S.243, B:S.243, B:S.243 Salt bridges: B:R.241 CPL.19: 7 residues within 4Å: Chain B: L.133, Y.137, E.139, L.142, N.143, L.146 Ligands: CPL.17 No protein-ligand interaction detected (PLIP) CPL.22: 7 residues within 4Å: Chain C: F.152, Q.156, Y.176, I.177, I.180, I.258, T.261 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.152, C:Y.176, C:Y.176, C:I.180, C:I.258, C:T.261 CPL.23: 6 residues within 4Å: Chain C: V.187, S.190, I.191, A.194 Ligands: CPL.24, CPL.25 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.187 CPL.24: 10 residues within 4Å: Chain C: I.191, A.194, I.195, R.241, S.243, V.246, F.247, V.250 Ligands: CPL.23, CPL.26 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.191, C:V.246, C:F.247 CPL.25: 14 residues within 4Å: Chain C: I.54, A.57, C.58, D.60, N.136, Y.137, E.139, L.142, W.183, V.187, S.190, K.193 Ligands: CPL.23, CPL.27 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.54, C:Y.137, C:E.139, C:L.142, C:W.183 Hydrogen bonds: C:S.190 Salt bridges: C:K.193 CPL.26: 20 residues within 4Å: Chain B: V.174, V.178, E.211, R.214, A.216, R.217, Y.219, V.220, L.223 Chain C: R.241, D.242, S.243, V.246, V.249, V.250, L.253, I.254, L.257 Ligands: CLR.12, CPL.24 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:R.241, C:D.242, C:V.246, C:V.250, C:L.253, C:L.257, B:V.174, B:V.178, B:Y.219, B:Y.219, B:L.223 Hydrogen bonds: C:D.242, C:S.243, C:S.243, C:S.243 Salt bridges: C:R.241 CPL.27: 7 residues within 4Å: Chain C: L.133, Y.137, E.139, L.142, N.143, L.146 Ligands: CPL.25 No protein-ligand interaction detected (PLIP) CPL.30: 7 residues within 4Å: Chain D: F.152, Q.156, Y.176, I.177, I.180, I.258, T.261 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.152, D:Y.176, D:Y.176, D:I.180, D:I.258, D:T.261 CPL.31: 6 residues within 4Å: Chain D: V.187, S.190, I.191, A.194 Ligands: CPL.32, CPL.33 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.187 CPL.32: 10 residues within 4Å: Chain D: I.191, A.194, I.195, R.241, S.243, V.246, F.247, V.250 Ligands: CPL.31, CPL.34 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.191, D:V.246, D:F.247 CPL.33: 14 residues within 4Å: Chain D: I.54, A.57, C.58, D.60, N.136, Y.137, E.139, L.142, W.183, V.187, S.190, K.193 Ligands: CPL.31, CPL.35 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.54, D:Y.137, D:E.139, D:L.142, D:W.183 Hydrogen bonds: D:S.190 Salt bridges: D:K.193 CPL.34: 20 residues within 4Å: Chain C: V.174, V.178, E.211, R.214, A.216, R.217, Y.219, V.220, L.223 Chain D: R.241, D.242, S.243, V.246, V.249, V.250, L.253, I.254, L.257 Ligands: CLR.20, CPL.32 16 PLIP interactions: 5 interactions with chain C, 11 interactions with chain D Hydrophobic interactions: C:V.174, C:V.178, C:Y.219, C:Y.219, C:L.223, D:R.241, D:D.242, D:V.246, D:V.250, D:L.253, D:L.257 Hydrogen bonds: D:D.242, D:S.243, D:S.243, D:S.243 Salt bridges: D:R.241 CPL.35: 7 residues within 4Å: Chain D: L.133, Y.137, E.139, L.142, N.143, L.146 Ligands: CPL.33 No protein-ligand interaction detected (PLIP)

3 x K: POTASSIUM ION(Non-covalent)

K.9: 5 residues within 4Å: Chain A: T.232 Chain B: T.232 Chain C: T.232 Chain D: T.232 Ligands: K.10 No protein-ligand interaction detected (PLIP) K.10: 6 residues within 4Å: Chain A: I.233 Chain B: I.233 Chain C: I.233 Chain D: I.233 Ligands: K.9, K.11 No protein-ligand interaction detected (PLIP) K.11: 9 residues within 4Å: Chain A: I.233, E.235 Chain B: I.233, E.235 Chain C: I.233, E.235 Chain D: I.233, E.235 Ligands: K.10 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:E.235, D:E.235, A:E.235, C:E.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xue, J. et al., Structural mechanisms of gating and selectivity of human rod CNGA1 channel. Neuron (2021)

Release Date

2021-03-10

Peptides

cGMP-gated cation channel alpha-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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cGMP-gated cation channel alpha-1

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