5K47

CryoEM structure of the human Polycystin-2/PKD2 TRP channel


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

Structure of the polycystic kidney disease TRP channel Polycystin-2 (PC2).

Grieben, M.Pike, A.C.Shintre, C.A.Venturi, E.El-Ajouz, S.Tessitore, A.Shrestha, L.Mukhopadhyay, S.Mahajan, P.Chalk, R.Burgess-Brown, N.A.Sitsapesan, R.Huiskonen, J.T.Carpenter, E.P.

(2017) Nat. Struct. Mol. Biol. 24: 114-122

  • DOI: 10.1038/nsmb.3343

  • PubMed Abstract: 
  • Mutations in either polycystin-1 (PC1 or PKD1) or polycystin-2 (PC2, PKD2 or TRPP1) cause autosomal-dominant polycystic kidney disease (ADPKD) through unknown mechanisms. Here we present the structure of human PC2 in a closed conformation, solved by ...

    Mutations in either polycystin-1 (PC1 or PKD1) or polycystin-2 (PC2, PKD2 or TRPP1) cause autosomal-dominant polycystic kidney disease (ADPKD) through unknown mechanisms. Here we present the structure of human PC2 in a closed conformation, solved by electron cryomicroscopy at 4.2-Å resolution. The structure reveals a novel polycystin-specific 'tetragonal opening for polycystins' (TOP) domain tightly bound to the top of a classic transient receptor potential (TRP) channel structure. The TOP domain is formed from two extensions to the voltage-sensor-like domain (VSLD); it covers the channel's endoplasmic reticulum lumen or extracellular surface and encloses an upper vestibule, above the pore filter, without blocking the ion-conduction pathway. The TOP-domain fold is conserved among the polycystins, including the homologous channel-like region of PC1, and is the site of a cluster of ADPKD-associated missense variants. Extensive contacts among the TOP-domain subunits, the pore and the VSLD provide ample scope for regulation through physical and chemical stimuli.


    Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polycystin-2
A, B, C, D
547Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom092809/Z/10/Z

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2017-01-11
    Type: Database references
  • Version 1.3: 2017-02-15
    Type: Database references
  • Version 1.4: 2017-08-30
    Type: Data collection, Experimental preparation
  • Version 1.5: 2018-10-03
    Type: Data collection, Refinement description
  • Version 1.6: 2018-10-10
    Type: Data collection, Refinement description, Structure summary