5MKE

cryoEM Structure of Polycystin-2 in complex with cations and lipids


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Molecular insights into lipid-assisted Ca(2+) regulation of the TRP channel Polycystin-2.

Wilkes, M.Madej, M.G.Kreuter, L.Rhinow, D.Heinz, V.De Sanctis, S.Ruppel, S.Richter, R.M.Joos, F.Grieben, M.Pike, A.C.Huiskonen, J.T.Carpenter, E.P.Kuhlbrandt, W.Witzgall, R.Ziegler, C.

(2017) Nat Struct Mol Biol 24: 123-130

  • DOI: 10.1038/nsmb.3357
  • Primary Citation of Related Structures:  
    5MKF, 5MKE

  • PubMed Abstract: 
  • Polycystin-2 (PC2), a calcium-activated cation TRP channel, is involved in diverse Ca 2+ signaling pathways. Malfunctioning Ca 2+ regulation in PC2 causes autosomal-dominant polycystic kidney disease. Here we report two cryo-EM structures of distinct channel states of full-length human PC2 in complex with lipids and cations ...

    Polycystin-2 (PC2), a calcium-activated cation TRP channel, is involved in diverse Ca 2+ signaling pathways. Malfunctioning Ca 2+ regulation in PC2 causes autosomal-dominant polycystic kidney disease. Here we report two cryo-EM structures of distinct channel states of full-length human PC2 in complex with lipids and cations. The structures reveal conformational differences in the selectivity filter and in the large exoplasmic domain (TOP domain), which displays differing N-glycosylation. The more open structure has one cation bound below the selectivity filter (single-ion mode, PC2 SI ), whereas multiple cations are bound along the translocation pathway in the second structure (multi-ion mode, PC2 MI ). Ca 2+ binding at the entrance of the selectivity filter suggests Ca 2+ blockage in PC2 MI , and we observed density for the Ca 2+ -sensing C-terminal EF hand in the unblocked PC2 SI state. The states show altered interactions of lipids with the pore loop and TOP domain, thus reflecting the functional diversity of PC2 at different locations, owing to different membrane compositions.


    Organizational Affiliation

    Biophysics II, Faculty of Biology and Preclinical Medicine, Regensburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polycystin-2A, B, C, D968Homo sapiensMutation(s): 0 
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
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, G2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PX6
Query on PX6

Download Ideal Coordinates CCD File 
DA [auth C], L [auth A], NA [auth D], V [auth B]1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
C35 H68 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-M
 Ligand Interaction
PLM
Query on PLM

Download Ideal Coordinates CCD File 
EA [auth C] , FA [auth C] , GA [auth C] , M [auth A] , N [auth A] , O [auth A] , OA [auth D] , PA [auth D] , 
EA [auth C],  FA [auth C],  GA [auth C],  M [auth A],  N [auth A],  O [auth A],  OA [auth D],  PA [auth D],  QA [auth D],  W [auth B],  X [auth B],  Y [auth B]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C] , H [auth A] , HA [auth D] , I [auth A] , IA [auth D] , JA [auth D] , KA [auth D] , R [auth B] , 
AA [auth C],  H [auth A],  HA [auth D],  I [auth A],  IA [auth D],  JA [auth D],  KA [auth D],  R [auth B],  S [auth B],  Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CHS
Query on CHS

Download Ideal Coordinates CCD File 
BA [auth C], CA [auth C], J [auth A], K [auth A], LA [auth D], MA [auth D], T [auth B], U [auth B]4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID
C11 H21 N O3
UQWNNUPJBDWRHC-UWVGGRQHSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
P [auth A], Q [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2017-02-15
    Changes: Database references
  • Version 1.3: 2019-12-11
    Changes: Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary