SMTL ID : 6t9n.1

CryoEM structure of human polycystin-2/PKD2 in UDM supplemented with PI(4,5)P2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 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: 7 residues within 4Å: Chain A: R.137, D.190, L.191, N.192, Y.209, Q.354, N.364 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.354 NAG-NAG.2: 7 residues within 4Å: Chain B: R.137, D.190, L.191, N.192, Y.209, Q.354, N.364 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.354 NAG-NAG.3: 7 residues within 4Å: Chain C: R.137, D.190, L.191, N.192, Y.209, Q.354, N.364 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.354 NAG-NAG.4: 7 residues within 4Å: Chain D: R.137, D.190, L.191, N.192, Y.209, Q.354, N.364 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.354

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 13 residues within 4Å: Chain A: L.327, V.330, L.334, Q.374, N.377, I.378, V.381, F.385 Chain B: V.472, L.473, I.476 Ligands: UMQ.8, UMQ.10 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.327, A:V.330, A:V.330, A:L.334, A:I.378, A:V.381, A:V.381, A:F.385, A:F.385, B:V.472, B:L.473, B:I.476 Hydrogen bonds: A:Q.374, A:Q.374, A:N.377 CLR.18: 13 residues within 4Å: Chain B: L.327, V.330, L.334, Q.374, N.377, I.378, V.381, F.385 Chain C: V.472, L.473, I.476 Ligands: UMQ.21, UMQ.23 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.327, B:V.330, B:V.330, B:L.334, B:I.378, B:V.381, B:V.381, B:F.385, B:F.385, C:V.472, C:L.473, C:I.476 Hydrogen bonds: B:Q.374, B:Q.374, B:N.377 CLR.28: 13 residues within 4Å: Chain C: L.327, V.330, L.334, Q.374, N.377, I.378, V.381, F.385 Chain D: V.472, L.473, I.476 Ligands: UMQ.31, UMQ.33 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.327, C:V.330, C:V.330, C:L.334, C:I.378, C:V.381, C:V.381, C:F.385, C:F.385, D:V.472, D:I.476 Hydrogen bonds: C:Q.374, C:Q.374, C:N.377 CLR.39: 13 residues within 4Å: Chain A: V.472, L.473, I.476 Chain D: L.327, V.330, L.334, Q.374, N.377, I.378, V.381, F.385 Ligands: UMQ.42, UMQ.44 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.327, D:V.330, D:V.330, D:L.334, D:I.378, D:V.381, D:V.381, D:F.385, D:F.385, A:V.472, A:I.476 Hydrogen bonds: D:Q.374, D:Q.374, D:N.377

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 3 residues within 4Å: Chain A: N.145, E.160, Y.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.145, A:E.160 NAG.7: 3 residues within 4Å: Chain A: P.177, N.179, N.229 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.177 Hydrogen bonds: A:N.229 NAG.19: 3 residues within 4Å: Chain B: N.145, E.160, Y.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.145, B:E.160 NAG.20: 3 residues within 4Å: Chain B: P.177, N.179, N.229 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.177 Hydrogen bonds: B:N.229 NAG.29: 3 residues within 4Å: Chain C: N.145, E.160, Y.162 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.145, C:E.160 NAG.30: 3 residues within 4Å: Chain C: P.177, N.179, N.229 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.177 Hydrogen bonds: C:N.229 NAG.40: 3 residues within 4Å: Chain D: N.145, E.160, Y.162 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.145, D:E.160 NAG.41: 3 residues within 4Å: Chain D: P.177, N.179, N.229 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:P.177 Hydrogen bonds: D:N.229

32 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.8: 14 residues within 4Å: Chain A: H.196, W.197, Q.273, Y.370, I.373, Q.374, N.377 Chain B: A.469, N.470, R.471, V.472 Ligands: CLR.5, UMQ.10, UMQ.11 Ligand excluded by PLIP UMQ.9: 13 residues within 4Å: Chain A: L.51, L.54, M.58, Y.282, E.294, F.297, A.338, I.339, N.342, I.343, S.347, F.375, A.379 Ligand excluded by PLIP UMQ.10: 7 residues within 4Å: Chain A: W.197, T.202 Chain B: V.472, I.476 Ligands: CLR.5, UMQ.8, UMQ.12 Ligand excluded by PLIP UMQ.11: 9 residues within 4Å: Chain A: S.194, S.195, V.333, L.334, H.367, Y.370, W.371, Q.374 Ligands: UMQ.8 Ligand excluded by PLIP UMQ.12: 7 residues within 4Å: Chain A: W.197, Q.447, F.451 Chain B: R.471, P.475, I.476 Ligands: UMQ.10 Ligand excluded by PLIP UMQ.13: 10 residues within 4Å: Chain A: L.426, Q.430, Y.433, F.446 Chain D: T.55, Y.56, M.59, S.60, S.61, W.387 Ligand excluded by PLIP UMQ.14: 9 residues within 4Å: Chain A: F.323, W.324, I.388, F.391, S.404, M.407, S.408 Chain B: I.424 Ligands: UMQ.15 Ligand excluded by PLIP UMQ.15: 4 residues within 4Å: Chain A: F.323, S.408, A.411 Ligands: UMQ.14 Ligand excluded by PLIP UMQ.16: 9 residues within 4Å: Chain A: T.55, Y.56, M.59, S.61, W.387 Chain B: L.426, Q.430, Y.433, F.446 Ligand excluded by PLIP UMQ.21: 14 residues within 4Å: Chain B: H.196, W.197, Q.273, Y.370, I.373, Q.374, N.377 Chain C: A.469, N.470, R.471, V.472 Ligands: CLR.18, UMQ.23, UMQ.24 Ligand excluded by PLIP UMQ.22: 12 residues within 4Å: Chain B: L.51, L.54, Y.282, E.294, F.297, A.338, I.339, N.342, I.343, S.347, F.375, A.379 Ligand excluded by PLIP UMQ.23: 7 residues within 4Å: Chain B: W.197, T.202 Chain C: V.472, I.476 Ligands: CLR.18, UMQ.21, UMQ.25 Ligand excluded by PLIP UMQ.24: 9 residues within 4Å: Chain B: S.194, S.195, V.333, L.334, H.367, Y.370, W.371, Q.374 Ligands: UMQ.21 Ligand excluded by PLIP UMQ.25: 7 residues within 4Å: Chain B: W.197, Q.447, F.451 Chain C: R.471, P.475, I.476 Ligands: UMQ.23 Ligand excluded by PLIP UMQ.26: 9 residues within 4Å: Chain B: F.323, W.324, I.388, F.391, S.404, M.407, S.408 Chain C: I.424 Ligands: UMQ.27 Ligand excluded by PLIP UMQ.27: 4 residues within 4Å: Chain B: F.323, S.408, A.411 Ligands: UMQ.26 Ligand excluded by PLIP UMQ.31: 14 residues within 4Å: Chain C: H.196, W.197, Q.273, Y.370, I.373, Q.374, N.377 Chain D: A.469, N.470, R.471, V.472 Ligands: CLR.28, UMQ.33, UMQ.34 Ligand excluded by PLIP UMQ.32: 12 residues within 4Å: Chain C: L.51, L.54, Y.282, E.294, F.297, A.338, I.339, N.342, I.343, S.347, F.375, A.379 Ligand excluded by PLIP UMQ.33: 7 residues within 4Å: Chain C: W.197, T.202 Chain D: V.472, I.476 Ligands: CLR.28, UMQ.31, UMQ.35 Ligand excluded by PLIP UMQ.34: 9 residues within 4Å: Chain C: S.194, S.195, V.333, L.334, H.367, Y.370, W.371, Q.374 Ligands: UMQ.31 Ligand excluded by PLIP UMQ.35: 7 residues within 4Å: Chain C: W.197, Q.447, F.451 Chain D: R.471, P.475, I.476 Ligands: UMQ.33 Ligand excluded by PLIP UMQ.36: 9 residues within 4Å: Chain B: T.55, Y.56, M.59, S.61, W.387 Chain C: L.426, Q.430, Y.433, F.446 Ligand excluded by PLIP UMQ.37: 9 residues within 4Å: Chain C: F.323, W.324, I.388, F.391, S.404, M.407, S.408 Chain D: I.424 Ligands: UMQ.38 Ligand excluded by PLIP UMQ.38: 4 residues within 4Å: Chain C: F.323, S.408, A.411 Ligands: UMQ.37 Ligand excluded by PLIP UMQ.42: 14 residues within 4Å: Chain A: A.469, N.470, R.471, V.472 Chain D: H.196, W.197, Q.273, Y.370, I.373, Q.374, N.377 Ligands: CLR.39, UMQ.44, UMQ.45 Ligand excluded by PLIP UMQ.43: 12 residues within 4Å: Chain D: L.51, L.54, Y.282, E.294, F.297, A.338, I.339, N.342, I.343, S.347, F.375, A.379 Ligand excluded by PLIP UMQ.44: 7 residues within 4Å: Chain A: V.472, I.476 Chain D: W.197, T.202 Ligands: CLR.39, UMQ.42, UMQ.46 Ligand excluded by PLIP UMQ.45: 9 residues within 4Å: Chain D: S.194, S.195, V.333, L.334, H.367, Y.370, W.371, Q.374 Ligands: UMQ.42 Ligand excluded by PLIP UMQ.46: 7 residues within 4Å: Chain A: R.471, P.475, I.476 Chain D: W.197, Q.447, F.451 Ligands: UMQ.44 Ligand excluded by PLIP UMQ.47: 9 residues within 4Å: Chain C: T.55, Y.56, M.59, S.61, W.387 Chain D: L.426, Q.430, Y.433, F.446 Ligand excluded by PLIP UMQ.48: 9 residues within 4Å: Chain A: I.424 Chain D: F.323, W.324, I.388, F.391, S.404, M.407, S.408 Ligands: UMQ.49 Ligand excluded by PLIP UMQ.49: 4 residues within 4Å: Chain D: F.323, S.408, A.411 Ligands: UMQ.48 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.17: 4 residues within 4Å: Chain A: L.458 Chain B: L.458 Chain C: L.458 Chain D: L.458 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Metal complexes: A:L.458, B:L.458, C:L.458, D:L.458

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q. et al., Lipid Interactions of a Ciliary Membrane TRP Channel: Simulation and Structural Studies of Polycystin-2. Structure (2020)

Release Date

2019-11-20

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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