6D1W | pdb_00006d1w

human PKD2 F604P mutant

• PDB DOI: https://doi.org/10.2210/pdb6D1W/pdb
• EM Map EMD-7786: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2018-04-12 Released: 2018-06-27 
• Deposition Author(s): Zheng, W., Yang, X., Bulkley, D., Chen, X.Z., Cao, E.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

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

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

• PubMed: 29899465 
• DOI: https://doi.org/10.1038/s41467-018-04586-x
• Primary Citation 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. 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.

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Organizational Affiliation: 
• National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, Hubei, 430068, China.
Department of Physiology, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
Experimentelle und Klinische Pharmakologie und Toxikologie, Universität des Saarlandes, Homburg, 66421, Germany.
Department of Biological Sciences, St. John's University, Queens, NY, 11439, USA.
Keck Advanced Microscopy Laboratory and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94143, USA.
National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, Hubei, 430068, China. [e-mail].
Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA. [e-mail].
National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, Hubei, 430068, China. [e-mail].
Department of Physiology, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 342.64 kDa 
• Atom Count: 14,492 
• Modeled Residue Count: 1,804 
• Deposited Residue Count: 2,960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycystin-2	A, B, C, D	740	Homo sapiens	Mutation(s): 1  Gene Names: PKD2, TRPP2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q13563 (Homo sapiens) Explore Q13563  Go to UniProtKB:  Q13563
PHAROS:  Q13563 GTEx:  ENSG00000118762
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: Q13563-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-27 
Deposition Author(s): Zheng, W., Yang, X., Bulkley, D., Chen, X.Z., Cao, E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01 DK110575-01

Revision History  

• 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
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2025-05-21
  Changes: Data collection