Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 240371.08 
• Atom Count: 14876 
• Residue Count: 2040 
• Unique protein chains: 1

5T4D

Cryo-EM structure of Polycystic Kidney Disease protein 2 (PKD2), residues 198-703

• DOI: 10.2210/pdb5T4D/pdb
• EMDataResource: EMD-8354

• Classification: METAL TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Homo sapiens


• Deposited: 2016-08-29 Released: 2016-11-02 
• Deposition Author(s): Shen, P.S., Yang, X., DeCaen, P.G., Liu, X., Bulkley, D., Clapham, D.E., Cao, E.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The Structure of the Polycystic Kidney Disease Channel PKD2 in Lipid Nanodiscs.

Shen, P.S., Yang, X., DeCaen, P.G., Liu, X., Bulkley, D., Clapham, D.E., Cao, E.

(2016) Cell 167: 763-773.e11

• PubMed: 27768895 
• DOI: 10.1016/j.cell.2016.09.048


• PubMed Abstract: 
  

The Polycystic Kidney Disease 2 (Pkd2) gene is mutated in autosomal dominant polycystic kidney disease (ADPKD), one of the most common human monogenic disorders. Here, we present the cryo-EM structure of PKD2 in lipid bilayers at 3.0 Å resolution, which establishes PKD2 as a homotetrameric ion channel and provides insight into potential mechanisms for its activation. The PKD2 voltage-sensor domain retains two of four gating charges commonly found in those of voltage-gated ion channels. The PKD2 ion permeation pathway is constricted at the selectivity filter and near the cytoplasmic end of S6, suggesting that two gates regulate ion conduction. The extracellular domain of PKD2, a hotspot for ADPKD pathogenic mutations, contributes to channel assembly and strategically interacts with the transmembrane core, likely serving as a physical substrate for extracellular stimuli to allosterically gate the channel. Finally, our structure establishes the molecular basis for the majority of pathogenic mutations in Pkd2-related ADPKD.

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Organizational Affiliation: 

Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
hPKD:198-703, Polycystin-2	A, B, C, D	510	Homo sapiens	Mutation(s): 0  Gene Names: PKD2 (TRPP2)
Membrane protein mpstruc	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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAG	A, B, C, D	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-08-29 
• Released Date: 2016-11-02 
• Deposition Author(s): Shen, P.S., Yang, X., DeCaen, P.G., Liu, X., Bulkley, D., Clapham, D.E., Cao, E.

Revision History 

• Version 1.0: 2016-11-02
  Type: Initial release
• Version 1.1: 2016-11-09
  Type: Structure summary
• Version 1.2: 2016-11-30
  Type: Structure summary
• Version 1.3: 2017-11-08
  Type: Data processing, Derived calculations
• Version 1.4: 2019-11-06
  Type: Data collection, Other