Biological Assembly 1  

 3D View: Structure | Ligand Interaction | Predict Membrane 

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

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

Macromolecule Content

• Total Structure Weight: 259.41 kDa 
• Atom Count: 15680 
• Modelled Residue Count: 1936 
• Deposited Residue Count: 2188 
• Unique protein chains: 1

5K47

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

• DOI: 10.2210/pdb5K47/pdb
• EMDataResource: EMD-8200

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2016-05-20 Released: 2016-08-24 
• Deposition Author(s): Pike, A.C.W., Grieben, M., Shintre, C.A., Tessitore, A., Shrestha, L., Mukhopadhyay, S., Mahajan, P., Chalk, R., Burgess-Brown, N.A., Huiskonen, J.T., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Carpenter, E.P., Structural Genomics Consortium (SGC)
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

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

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

• PubMed: 27991905 
• 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 4.2-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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycystin-2	A, B, C, D	547	Homo sapiens	Mutation(s): 0  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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], 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: 4.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-05-20 
• Released Date: 2016-08-24 
Deposition Author(s): Pike, A.C.W., Grieben, M., Shintre, C.A., Tessitore, A., Shrestha, L., Mukhopadhyay, S., Mahajan, P., Chalk, R., Burgess-Brown, N.A., Huiskonen, J.T., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Carpenter, E.P., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	092809/Z/10/Z

Revision History  

• 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