8Z6F | pdb_00008z6f

Structure of polycystin-1/polycystin-2 complex with PI(4)P-bound

• PDB DOI: https://doi.org/10.2210/pdb8Z6F/pdb
• EM Map EMD-39798: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-04-19 Released: 2025-04-23 
• Deposition Author(s): Chen, M.Y., Su, Q., Shi, Y.G.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.08 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of polycystin-1/polycystin-2 complex with PI(4)P-bound

Chen, M., Su, Q., Shi, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 480.07 kDa 
• Atom Count: 17,299 
• Modeled Residue Count: 2,172 
• Deposited Residue Count: 4,282 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycystin-1	A	1,261	Homo sapiens	Mutation(s): 0  Gene Names: PKD1
UniProt & NIH Common Fund Data Resources
Find proteins for P98161 (Homo sapiens) Explore P98161  Go to UniProtKB:  P98161
PHAROS:  P98161 GTEx:  ENSG00000008710

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycystin-2	B, C, D	1,007	Homo sapiens	Mutation(s): 0  Gene Names: PKD2, TRPP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13563 (Homo sapiens) Explore Q13563  Go to UniProtKB:  Q13563
PHAROS:  Q13563 GTEx:  ENSG00000118762

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D75 (Subject of Investigation/LOI)	E [auth A]	[(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate C41 H80 O16 P2 UJVUMTUBMCYKBK-SDTPXLKLSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.08 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: 2025-04-23 
Deposition Author(s): Chen, M.Y., Su, Q., Shi, Y.G.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31930059
National Natural Science Foundation of China (NSFC)	China	81920108015

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release
  
• Version 1.1: 2025-07-16
  Changes: Data collection