5Z1W

Cryo-EM structure of polycystic kidney disease-like channel PKD2L1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 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

Cryo-EM structure of the polycystic kidney disease-like channel PKD2L1.

Su, Q.Hu, F.Liu, Y.Ge, X.Mei, C.Yu, S.Shen, A.Zhou, Q.Yan, C.Lei, J.Zhang, Y.Liu, X.Wang, T.

(2018) Nat Commun 9: 1192-1192

  • DOI: 10.1038/s41467-018-03606-0
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • PKD2L1, also termed TRPP3 from the TRPP subfamily (polycystic TRP channels), is involved in the sour sensation and other pH-dependent processes. PKD2L1 is believed to be a nonselective cation channel that can be regulated by voltage, protons, and cal ...

    PKD2L1, also termed TRPP3 from the TRPP subfamily (polycystic TRP channels), is involved in the sour sensation and other pH-dependent processes. PKD2L1 is believed to be a nonselective cation channel that can be regulated by voltage, protons, and calcium. Despite its considerable importance, the molecular mechanisms underlying PKD2L1 regulations are largely unknown. Here, we determine the PKD2L1 atomic structure at 3.38 Å resolution by cryo-electron microscopy, whereby side chains of nearly all residues are assigned. Unlike its ortholog PKD2, the pore helix (PH) and transmembrane segment 6 (S6) of PKD2L1, which are involved in upper and lower-gate opening, adopt an open conformation. Structural comparisons of PKD2L1 with a PKD2-based homologous model indicate that the pore domain dilation is coupled to conformational changes of voltage-sensing domains (VSDs) via a series of π-π interactions, suggesting a potential PKD2L1 gating mechanism.


    Organizational Affiliation

    Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polycystic kidney disease 2-like 1 proteinA, B, C, D566Mus musculusMutation(s): 0 
Gene Names: Pkd2l1Trpp3
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Transient Receptor Potential (TRP)
Protein: 
PKD2L1 polycystic kidney disease channel (residues 64-629)
Find proteins for A2A259 (Mus musculus)
Explore A2A259 
Go to UniProtKB:  A2A259
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, C, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-12-28 
  • Released Date: 2018-03-28 
  • Deposition Author(s): Zhang, Y.Q.

Funding OrganizationLocationGrant Number
China--

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary