8ZKT | pdb_00008zkt

Structure of Polycystin-1/Polycystin-2 complex with GOF mutations

• PDB DOI: https://doi.org/10.2210/pdb8ZKT/pdb
• EM Map EMD-60208: EMDB EMDataResource

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


• Deposited: 2024-05-17 Released: 2025-05-21 
• Deposition Author(s): Chen, M.Y., Su, Q., Shi, Y.G.
• 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 Polycystin-1/Polycystin-2 complex with GOF mutations

Chen, M.Y., Su, Q., Shi, Y.G.

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: 481.17 kDa 
• Atom Count: 17,369 
• Modeled Residue Count: 2,166 
• 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
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], K [auth D], L [auth D], M [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: 3.34 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: 2025-05-21 
Deposition Author(s): Chen, M.Y., Su, Q., Shi, Y.G.

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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

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release
  
• Version 2.0: 2025-06-11
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2025-07-23
  Changes: Data collection