SMTL ID : 5mke.1

cryoEM Structure of Polycystin-2 in complex with cations and lipids

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.30 Å

Oligo State

homo-tetramer

Ligands

3 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: D.373, N.375, L.539 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: D.373, N.375, L.539 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: D.373, N.375, L.539 No protein-ligand interaction detected (PLIP)

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.4: 3 residues within 4Å: Chain A: N.305, R.397, T.398 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.397, A:T.398, A:T.398 NAG.5: 6 residues within 4Å: Chain A: P.360, R.361, N.362, S.408, K.411, N.412 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.408, A:K.411 NAG.14: 3 residues within 4Å: Chain B: N.305, R.397, T.398 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.397, B:T.398, B:T.398 NAG.15: 6 residues within 4Å: Chain B: P.360, R.361, N.362, S.408, K.411, N.412 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.408, B:K.411 NAG.22: 4 residues within 4Å: Chain C: N.305, R.397, T.398, N.543 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.397 NAG.23: 6 residues within 4Å: Chain C: P.360, R.361, N.362, S.408, K.411, N.412 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.408, C:K.411 NAG.30: 4 residues within 4Å: Chain D: N.305, R.397, T.398, N.543 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.397, D:T.398, D:T.398 NAG.31: 6 residues within 4Å: Chain D: P.360, R.361, N.362, S.408, K.411, N.412 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.408, D:K.411 NAG.32: 3 residues within 4Å: Chain D: D.373, N.375 Ligands: NAG.33 No protein-ligand interaction detected (PLIP) NAG.33: 2 residues within 4Å: Chain D: L.539 Ligands: NAG.32 No protein-ligand interaction detected (PLIP)

8 x CHS: 4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID(Non-covalent)

CHS.6: 4 residues within 4Å: Chain A: Y.239, W.570 Ligands: CHS.7, PLM.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.570 CHS.7: 5 residues within 4Å: Chain A: L.231, I.232, C.235, Y.239 Ligands: CHS.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.232 CHS.16: 4 residues within 4Å: Chain B: Y.239, W.570 Ligands: CHS.17, PLM.29 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.570 CHS.17: 5 residues within 4Å: Chain B: L.231, I.232, C.235, Y.239 Ligands: CHS.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.232 CHS.24: 4 residues within 4Å: Chain C: Y.239, W.570 Ligands: CHS.25, PLM.39 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.570 CHS.25: 5 residues within 4Å: Chain C: L.231, I.232, C.235, Y.239 Ligands: CHS.24 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.232 CHS.34: 4 residues within 4Å: Chain D: Y.239, W.570 Ligands: PLM.11, CHS.35 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.570 CHS.35: 5 residues within 4Å: Chain D: L.231, I.232, C.235, Y.239 Ligands: CHS.34 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.232

4 x PX6: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PX6.8: 9 residues within 4Å: Chain A: H.379, W.380, R.440, Q.456, Y.553, Q.557, N.560 Chain B: V.655 Ligands: PLM.11 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.380, A:Q.456 Salt bridges: A:H.379, A:R.440 Hydrophobic interactions: B:V.655 PX6.18: 9 residues within 4Å: Chain B: H.379, W.380, R.440, Q.456, Y.553, Q.557, N.560 Chain C: V.655 Ligands: PLM.21 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:W.380, B:Q.456 Salt bridges: B:H.379, B:R.440 Hydrophobic interactions: C:V.655 PX6.26: 9 residues within 4Å: Chain C: H.379, W.380, R.440, Q.456, Y.553, Q.557, N.560 Chain D: V.655 Ligands: PLM.29 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:W.380, C:Q.456 Salt bridges: C:H.379, C:R.440 Hydrophobic interactions: D:V.655 PX6.36: 9 residues within 4Å: Chain A: V.655 Chain D: H.379, W.380, R.440, Q.456, Y.553, Q.557, N.560 Ligands: PLM.39 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:W.380, D:Q.456 Salt bridges: D:H.379, D:R.440 Hydrophobic interactions: A:V.655

12 x PLM: PALMITIC ACID(Non-covalent)(Non-functional Binders)

PLM.9: 8 residues within 4Å: Chain A: F.567, M.590 Chain B: M.603, I.607, Y.611, I.659, T.663, F.667 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.607, B:I.659, B:T.663, B:F.667, A:F.567 PLM.10: 6 residues within 4Å: Chain A: W.380, F.605, Q.630 Chain B: R.654, T.662, F.666 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.662, B:F.666, B:F.666, A:F.605 Hydrogen bonds: A:Q.630 PLM.11: 2 residues within 4Å: Ligands: PX6.8, CHS.34 No protein-ligand interaction detected (PLIP) PLM.19: 8 residues within 4Å: Chain B: F.567, F.574, M.590 Chain C: M.603, I.607, Y.611, I.659, T.663 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.567, B:F.574, C:I.607, C:I.659, C:T.663 PLM.20: 6 residues within 4Å: Chain B: W.380, F.605, Q.630 Chain C: R.654, T.662, F.666 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:T.662, C:F.666, C:F.666, B:F.605 PLM.21: 2 residues within 4Å: Ligands: CHS.6, PX6.18 No protein-ligand interaction detected (PLIP) PLM.27: 8 residues within 4Å: Chain C: F.567, F.574, M.590 Chain D: M.603, I.607, Y.611, I.659, T.663 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.607, D:I.659, D:T.663, C:F.567, C:F.574 PLM.28: 6 residues within 4Å: Chain C: W.380, F.605, Q.630 Chain D: R.654, T.662, F.666 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.605, D:T.662, D:F.666, D:F.666 Hydrogen bonds: C:Q.630 PLM.29: 2 residues within 4Å: Ligands: CHS.16, PX6.26 No protein-ligand interaction detected (PLIP) PLM.37: 8 residues within 4Å: Chain A: M.603, I.607, Y.611, I.659, T.663 Chain D: F.567, F.574, M.590 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.607, A:I.659, A:T.663, D:F.567, D:F.574 PLM.38: 6 residues within 4Å: Chain A: R.654, T.662, F.666 Chain D: W.380, F.605, Q.630 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:F.605, A:T.662, A:F.666, A:F.666 Hydrogen bonds: D:Q.630 PLM.39: 2 residues within 4Å: Ligands: CHS.24, PX6.36 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-functional Binders)

CA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilkes, M. et al., Molecular insights into lipid-assisted Ca(2+) regulation of the TRP channel Polycystin-2. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-01-18

Peptides

Polycystin-2: 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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Polycystin-2

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