6DU8

Human Polycsytin 2-l1

• PDB DOI: https://doi.org/10.2210/pdb6DU8/pdb
• EM Map EMD-8912: EMDB EMDataResource

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


• Deposited: 2018-06-20 Released: 2018-07-25 
• Deposition Author(s): Hulse, R.E., Clapham, D.E., Li, Z., Huang, R.K., Zhang, J.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.11 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the polycystin 2-l1 ion channel.

Hulse, R.E., Li, Z., Huang, R.K., Zhang, J., Clapham, D.E.

(2018) Elife 7

• PubMed: 30004384 
• DOI: https://doi.org/10.7554/eLife.36931
• Primary Citation of Related Structures:  
  6DU8


• PubMed Abstract: 
  

  We report the near atomic resolution (3.3 Å) of the human polycystic kidney disease 2-like 1 (polycystin 2-l1) ion channel. Encoded by PKD2L1, polycystin 2-l1 is a calcium and monovalent cation-permeant ion channel in primary cilia and plasma membranes. The related primary cilium-specific polycystin-2 protein, encoded by PKD2, shares a high degree of sequence similarity, yet has distinct permeability characteristics. Here we show that these differences are reflected in the architecture of polycystin 2-l1.

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Organizational Affiliation: 

Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.

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: gel filtration

Macromolecule Content

• Total Structure Weight: 369.17 kDa 
• Atom Count: 13,380 
• Modelled Residue Count: 1,684 
• Deposited Residue Count: 3,220 
• 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	805	Homo sapiens	Mutation(s): 0  Gene Names: PKD2L1, PKD2L, PKDL, TRPP3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0L9 (Homo sapiens) Explore Q9P0L9  Go to UniProtKB:  Q9P0L9
PHAROS:  Q9P0L9 GTEx:  ENSG00000107593
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q9P0L9-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth B], G [auth C], H [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: 3.11 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Hulse, R.E., Clapham, D.E., Li, Z., Huang, R.K., Zhang, J.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Author supporting evidence
• Version 1.2: 2019-12-18
  Changes: Other
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary