5Z1W | pdb_00005z1w

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

• PDB DOI: https://doi.org/10.2210/pdb5Z1W/pdb
• EM Map EMD-6877: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


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

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Experimental Data Snapshot

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

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

• PubMed: 29567962 
• DOI: https://doi.org/10.1038/s41467-018-03606-0
• Primary Citation of Related Structures:  
  5Z1W


• 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 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.

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Organizational Affiliation: 
• Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China.
School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
School of Medicine, Tsinghua University, Beijing, 100084, China.
X-Lab for Transmembrane Signaling Research, Department of Biomedical Engineering and McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China.
School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China, 102402.
Department of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, 200433, China.
Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China. [e-mail].
School of Life Sciences, Tsinghua University, Beijing, 100084, China. [e-mail].
Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. [e-mail].
Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China. [e-mail].
School of Life Sciences, Tsinghua University, Beijing, 100084, China. [e-mail].
School of Medicine, Tsinghua University, Beijing, 100084, China. [e-mail].
X-Lab for Transmembrane Signaling Research, Department of Biomedical Engineering and McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China. [e-mail].
School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China. [e-mail].
Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China, 102402. [e-mail].
Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China. [e-mail].
Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. [e-mail].
School of Medicine, Tsinghua University, Beijing, 100084, China. [e-mail].
Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 265.06 kDa 
• Atom Count: 13,824 
• Modeled Residue Count: 1,716 
• Deposited Residue Count: 2,264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycystic kidney disease 2-like 1 protein	A, B, C, D	566	Mus musculus	Mutation(s): 0  Gene Names: Pkd2l1, Trpp3 Membrane Entity: Yes
UniProt
Find proteins for A2A259 (Mus musculus) Explore A2A259  Go to UniProtKB:  A2A259
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: A2A259-1

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: 3.38 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: 2018-03-28 
Deposition Author(s): Zhang, Y.Q.

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Funding Organization	Location	Grant 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
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2025-07-02
  Changes: Data collection