9IUI | pdb_00009iui

Crystal structure of PSD-95 GK domain in complex with GK_FingR

• PDB DOI: https://doi.org/10.2210/pdb9IUI/pdb

• Classification: PROTEIN BINDING
• Organism(s): Rattus norvegicus, unclassified sequences
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-21 Released: 2025-07-23 
• Deposition Author(s): Zhu, S., Cai, Q., Zhang, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Models: experimental

Literature

Modulating synaptic glutamate receptors by targeting network nodes of the postsynaptic density condensate.

Jia, B., Zhu, S., Shen, Z., Chen, X., Li, H., Zhao, S., Cai, Q., Wang, Y., Wang, Z., Nicoll, R.A., Lu, Y., Zhang, M.

(2025) Mol Cell 85: 3166

• PubMed: 40803326 
• DOI: https://doi.org/10.1016/j.molcel.2025.07.017
• Primary Citation Related Structures: 
  9IUI


• PubMed Abstract: 
  

  Biological condensates are assembled through phase separation and play critical roles in diverse cellular processes. Condensates in cells form percolated molecular networks via multi-valent interactions among biomolecules. How the network properties of a condensate are connected to its biological function is poorly understood. Using the neuronal postsynaptic density (PSD) condensate as a paradigm, we demonstrate thatbiological condensates can be bidirectionally modulated by strengthening or weakening different interaction nodes within the network. The clustering, mobility, and synaptic functions of AMPA receptors are exquisitely sensitive to alterations in the strength and complexity of the PSD condensate molecular network without changing the binding of the receptor to its direct downstream scaffold. Thus, biological condensates are complex systems with emergent network properties that are harnessed for cellular functions and in this case for synaptic plasticity.

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Organizational Affiliation: 
• School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
Department of Neurology and Institute of Neuroscience of Soochow University, Second Affiliated Hospital of Soochow University, Suzhou 215004, China; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA.
Department of Pathophysiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan 430030, China.
State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian 361102, China.
School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA.
School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.98 kDa 
• Atom Count: 4,667 
• Modeled Residue Count: 544 
• Deposited Residue Count: 570 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disks large homolog 4	A, C	189	Rattus norvegicus	Mutation(s): 0  Gene Names: Dlg4, Dlgh4, Psd95
UniProt
Find proteins for P31016 (Rattus norvegicus) Explore P31016  Go to UniProtKB:  P31016

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FingR targeting PSD-95	B, D	96	unclassified sequences	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	F [auth D]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	G [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	E [auth C], H [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.429	α = 90
b = 74.987	β = 90
c = 136.567	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Zhu, S., Cai, Q., Zhang, M.

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

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release
  
• Version 1.1: 2025-08-20
  Changes: Database references
• Version 1.2: 2025-08-27
  Changes: Database references
• Version 1.3: 2025-09-10
  Changes: Database references