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 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1016/j.celrep.2017.11.107
  • Primary Citation of 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Disks large homolog 4A [auth B],
B [auth A]
189Rattus norvegicusMutation(s): 0 
Gene Names: Dlg4Dlgh4Psd95
UniProt
Find proteins for P31016 (Rattus norvegicus)
Explore P31016 
Go to UniProtKB:  P31016
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31016
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SAPAP
C, D
15Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O14490 (Homo sapiens)
Explore O14490 
Go to UniProtKB:  O14490
PHAROS:  O14490
GTEx:  ENSG00000170579 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14490
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D 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 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.776α = 90
b = 84.063β = 90
c = 165.123γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)China31770779
National Science Foundation (NSF, United States)China31470733
National Science Foundation (NSF, United States)ChinaU1532121
Shanghai Municipal Science and Technology CommissionChina14YF1406700
the Minister of Science and Technology of ChinaChina2014CB910204
RGCHong Kong16103614
RGCHong Kong16149516
RGCHong KongAoE-M09-12

Revision History  (Full details and data files)

  • 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