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 2.1 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
  • Primary Citation of Related Structures:  
    5K47

  • 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 electron cryomicroscopy at 4 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polycystin-2A, B, C, D547Homo sapiensMutation(s): 0 
Gene Names: PKD2TRPP2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Transient Receptor Potential (TRP)
Protein: 
PKD2 polycystic kidney disease channel in detergent
Find proteins for Q13563 (Homo sapiens)
Explore Q13563 
Go to UniProtKB:  Q13563
NIH Common Fund Data Resources
PHAROS:  Q13563
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F, G, H2 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2017-01-11
    Changes: Database references
  • Version 1.3: 2017-02-15
    Changes: Database references
  • Version 1.4: 2017-08-30
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2018-10-03
    Changes: Data collection, Refinement description
  • Version 1.6: 2018-10-10
    Changes: Data collection, Refinement description, Structure summary
  • Version 1.7: 2019-12-11
    Changes: Other, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-10-21
    Changes: Data collection, Structure summary