6D1W

human PKD2 F604P mutant


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 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

Hydrophobic pore gates regulate ion permeation in polycystic kidney disease 2 and 2L1 channels.

Zheng, W.Yang, X.Hu, R.Cai, R.Hofmann, L.Wang, Z.Hu, Q.Liu, X.Bulkey, D.Yu, Y.Tang, J.Flockerzi, V.Cao, Y.Cao, E.Chen, X.Z.

(2018) Nat Commun 9: 2302-2302

  • DOI: 10.1038/s41467-018-04586-x
  • Primary Citation of Related Structures:  
    6D1W

  • PubMed Abstract: 
  • PKD2 and PKD1 genes are mutated in human autosomal dominant polycystic kidney disease. PKD2 can form either a homomeric cation channel or a heteromeric complex with the PKD1 receptor, presumed to respond to ligand(s) and/or mechanical stimuli. Here, we identify a two-residue hydrophobic gate in PKD2L1, and a single-residue hydrophobic gate in PKD2 ...

    PKD2 and PKD1 genes are mutated in human autosomal dominant polycystic kidney disease. PKD2 can form either a homomeric cation channel or a heteromeric complex with the PKD1 receptor, presumed to respond to ligand(s) and/or mechanical stimuli. Here, we identify a two-residue hydrophobic gate in PKD2L1, and a single-residue hydrophobic gate in PKD2. We find that a PKD2 gain-of-function gate mutant effectively rescues PKD2 knockdown-induced phenotypes in embryonic zebrafish. The structure of a PKD2 activating mutant F604P by cryo-electron microscopy reveals a π- to α-helix transition within the pore-lining helix S6 that leads to repositioning of the gate residue and channel activation. Overall the results identify hydrophobic gates and a gating mechanism of PKD2 and PKD2L1.


    Organizational Affiliation

    Department of Physiology, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada. xzchen@ualberta.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polycystin-2A, B, C, D740Homo sapiensMutation(s): 1 
Gene Names: PKD2TRPP2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13563 (Homo sapiens)
Explore Q13563 
Go to UniProtKB:  Q13563
PHAROS:  Q13563
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01 DK110575-01

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary