5YPR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.349 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1016/j.celrep.2017.11.107
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    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.,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.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 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.,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: mzhang@ust.hk.,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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Disks large homolog 4
A
318Rattus norvegicusMutation(s): 0 
Gene Names: Dlg4 (Dlgh4, Psd95)
Find proteins for P31016 (Rattus norvegicus)
Go to UniProtKB:  P31016
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Synthesized GK inhibitor
B
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.349 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 119.028α = 90.00
b = 45.743β = 103.22
c = 86.358γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXphasing
HKL-3000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NSFChina31770779, 31470733 and U1532121
Shanghai Municipal Science and Technology CommissionChina14YF1406700
RGCHong Kong16103614, 16149516 and AoE-M09-12
the Minister of Science and Technology of ChinaChina2014CB910204

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release