5MKF

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular insights into lipid-assisted Ca(2+) regulation of the TRP channel Polycystin-2.

Wilkes, M.Madej, M.G.Kreuter, L.Rhinow, D.Heinz, V.De Sanctis, S.Ruppel, S.Richter, R.M.Joos, F.Grieben, M.Pike, A.C.Huiskonen, J.T.Carpenter, E.P.Kuhlbrandt, W.Witzgall, R.Ziegler, C.

(2017) Nat. Struct. Mol. Biol. 24: 123-130

  • DOI: 10.1038/nsmb.3357
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polycystin-2 (PC2), a calcium-activated cation TRP channel, is involved in diverse Ca <sup>2+ </sup> signaling pathways. Malfunctioning Ca <sup>2+ </sup> regulation in PC2 causes autosomal-dominant polycystic kidney disease. Here we report two cryo-E ...

    Polycystin-2 (PC2), a calcium-activated cation TRP channel, is involved in diverse Ca 2+ signaling pathways. Malfunctioning Ca 2+ regulation in PC2 causes autosomal-dominant polycystic kidney disease. Here we report two cryo-EM structures of distinct channel states of full-length human PC2 in complex with lipids and cations. The structures reveal conformational differences in the selectivity filter and in the large exoplasmic domain (TOP domain), which displays differing N-glycosylation. The more open structure has one cation bound below the selectivity filter (single-ion mode, PC2 SI ), whereas multiple cations are bound along the translocation pathway in the second structure (multi-ion mode, PC2 MI ). Ca 2+ binding at the entrance of the selectivity filter suggests Ca 2+ blockage in PC2 MI , and we observed density for the Ca 2+ -sensing C-terminal EF hand in the unblocked PC2 SI state. The states show altered interactions of lipids with the pore loop and TOP domain, thus reflecting the functional diversity of PC2 at different locations, owing to different membrane compositions.


    Organizational Affiliation

    Max Planck Institute of Biophysics, Department of Structural Biology, Frankfurt, Germany.,Structural Genomics Consortium, University of Oxford, Oxford, UK.,Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Department of Anatomy, Faculty of Biology and Preclinical Medicine, Regensburg, Germany.,Biophysics II, Faculty of Biology and Preclinical Medicine, Regensburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polycystin-2
A, B, C, D
968Homo sapiensMutation(s): 0 
Gene Names: PKD2 (TRPP2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Transient Receptor Potential (TRP)
Protein: 
PKD2 polycystic kidney disease channel in lipid nanodiscs
Find proteins for Q13563 (Homo sapiens)
Go to Gene View: PKD2
Go to UniProtKB:  Q13563
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PX6
Query on PX6

Download SDF File 
Download CCD File 
A, B, C, D
1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
C35 H68 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CHS
Query on CHS

Download SDF File 
Download CCD File 
A, B, C, D
4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID
C11 H21 N O3
UQWNNUPJBDWRHC-UWVGGRQHSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PLM
Query on PLM

Download SDF File 
Download CCD File 
A, B, C, D
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Database references
  • Version 1.2: 2017-02-15
    Type: Database references