9L0M | pdb_00009l0m

Structure of gain-of-function polycystin-1/polycystin-2 complex

• PDB DOI: https://doi.org/10.2210/pdb9L0M/pdb
• EM Map EMD-62719: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-12-12 Released: 2025-12-17 
• Deposition Author(s): Chen, M.Y., Su, Q., Chen, M.Y., Su, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.34 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of gain-of-function polycystin-1/polycystin-2 complex.

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: 479.9 kDa 
• Atom Count: 16,256 
• Modeled Residue Count: 2,181 
• Deposited Residue Count: 4,277 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycystin-1	A	1,262	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	1,005	Homo sapiens	Mutation(s): 2  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
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: Q13563-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth B], F [auth B], G [auth B], H [auth C], I [auth C], J [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.34 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Chen, M.Y., Su, Q., Chen, M.Y., Su, Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31930059
National Natural Science Foundation of China (NSFC)	China	81970633
National Natural Science Foundation of China (NSFC)	China	U1904146
National Natural Science Foundation of China (NSFC)	China	81920108015

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release