5YPR | pdb_00005ypr

Crystal Structure of PSD-95 SH3-GK domain in complex with a synthesized inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5YPR/pdb

• Classification: PROTEIN BINDING
• Organism(s): Rattus norvegicus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-11-02 Released: 2018-03-14 
• Deposition Author(s): Zhu, J., Zhou, Q., Shang, Y., Weng, Z., Zhu, R., Zhang, M.
• Funding Organization(s): National Science Foundation (NSF, United States), Shanghai Municipal Science and Technology Commission, RGC, the Minister of Science and Technology of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.264 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Synaptic Targeting and Function of SAPAPs Mediated by Phosphorylation-Dependent Binding to PSD-95 MAGUKs.

Zhu, J., Zhou, Q., Shang, Y., Li, H., Peng, M., Ke, X., Weng, Z., Zhang, R., Huang, X., Li, S.S.C., Feng, G., Lu, Y., Zhang, M.

(2017) Cell Rep 21: 3781-3793

• PubMed: 29281827 
• DOI: https://doi.org/10.1016/j.celrep.2017.11.107
• Primary Citation Related Structures: 
  5YPO, 5YPR


• PubMed Abstract: 
  

  The PSD-95/SAPAP/Shank complex functions as the major scaffold in orchestrating the formation and plasticity of the post-synaptic densities (PSDs). We previously demonstrated that the exquisitely specific SAPAP/Shank interaction is critical for Shank synaptic targeting and Shank-mediated synaptogenesis. Here, we show that the PSD-95/SAPAP interaction, SAPAP synaptic targeting, and SAPAP-mediated synaptogenesis require phosphorylation of the N-terminal repeat sequences of SAPAPs. The atomic structure of the PSD-95 guanylate kinase (GK) in complex with a phosphor-SAPAP repeat peptide, together with biochemical studies, reveals the molecular mechanism underlying the phosphorylation-dependent PSD-95/SAPAP interaction, and it also provides an explanation of a PSD-95 mutation found in patients with intellectual disabilities. Guided by the structural data, we developed potent non-phosphorylated GK inhibitory peptides capable of blocking the PSD-95/SAPAP interaction and interfering with PSD-95/SAPAP-mediated synaptic maturation and strength. These peptides are genetically encodable for investigating the functions of the PSD-95/SAPAP interaction in vivo.

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Organizational Affiliation: 
• National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201203, China; Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
Department of Physiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan 4030030, China; The Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan 430030, China.
National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201203, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
Department of Biochemistry, Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada.
McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 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: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 38.89 kDa 
• Atom Count: 2,257 
• Modeled Residue Count: 283 
• Deposited Residue Count: 334 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disks large homolog 4	A	318	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
Synthesized GK inhibitor	B	16	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.264 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.028	α = 90
b = 45.743	β = 103.22
c = 86.358	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Zhu, J., Zhou, Q., Shang, Y., Weng, Z., Zhu, R., Zhang, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	China	31770779, 31470733 and U1532121
Shanghai Municipal Science and Technology Commission	China	14YF1406700
RGC	Hong Kong	16103614, 16149516 and AoE-M09-12
the Minister of Science and Technology of China	China	2014CB910204

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2022-03-23
  Changes: Author supporting evidence, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary