5YPO

Crystal structure of PSD-95 GK domain in complex with phospho-SAPAP peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 

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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Disks large homolog 4
B, A
189Rattus norvegicusMutation(s): 0 
Gene Names: Dlg4 (Dlgh4, Psd95)
Find proteins for P31016 (Rattus norvegicus)
Go to UniProtKB:  P31016
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SAPAP
C, D
15Homo sapiensMutation(s): 0 
Gene Names: DLGAP1 (DAP1, GKAP)
Find proteins for O14490 (Homo sapiens)
Go to Gene View: DLGAP1
Go to UniProtKB:  O14490
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
C, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.776α = 90.00
b = 84.063β = 90.00
c = 165.123γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NSFChina31770779
NSFChina31470733
NSFChinaU1532121
Shanghai Municipal Science and Technology CommissionChina14YF1406700
the Minister of Science and Technology of ChinaChina2014CB910204
RGCHong Kong16103614
RGCHong Kong16149516
RGCHong KongAoE-M09-12

Revision History 

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