6J69

Structure of KIBRA and Dendrin Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Kibra Modulates Learning and Memory via Binding to Dendrin.

Ji, Z.Li, H.Yang, Z.Huang, X.Ke, X.Ma, S.Lin, Z.Lu, Y.Zhang, M.

(2019) Cell Rep 26: 2064-2077.e7

  • DOI: https://doi.org/10.1016/j.celrep.2019.01.097
  • Primary Citation of Related Structures:  
    6J69

  • PubMed Abstract: 

    Kibra is a synaptic scaffold protein regulating learning and memory. Alterations of Kibra-encoding gene WWC1 cause various neuronal disorders, including Alzheimer's disease and Tourette syndrome. However, the molecular mechanism underlying Kibra's function in neurons is poorly understood. Here we discover that Kibra, via its N-terminal WW12 tandem domains, binds to a postsynaptic density enriched protein, Dendrin, with a nanomolar dissociation constant. On the basis of the structure of Kibra WW12 in complex with Dendrin PY motifs, we developed a potent peptide inhibitor capable of specifically blocking the binding between Kibra and Dendrin in neurons. Systematic administration of the inhibitory peptide attenuated excitatory synaptic transmission, completely blocked long-term potentiation induction, and impaired spatial learning and memory. A Kibra mutation found in Tourette syndrome patients causes defects in binding to Dendrin. Thus, Kibra can modulate spatial learning and memory via binding to Dendrin.


  • Organizational Affiliation

    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
Protein KIBRA134Mus musculusMutation(s): 0 
Gene Names: Wwc1Kiaa0869
UniProt
Find proteins for Q5SXA9 (Mus musculus)
Explore Q5SXA9 
Go to UniProtKB:  Q5SXA9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SXA9
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Dendrin25Mus musculusMutation(s): 0 
Gene Names: DdnGm748Kiaa0749
UniProt
Find proteins for Q80TS7 (Mus musculus)
Explore Q80TS7 
Go to UniProtKB:  Q80TS7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80TS7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.443α = 90
b = 85.443β = 90
c = 80.566γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description