3K1R

Structure of harmonin NPDZ1 in complex with the SAM-PBM of Sans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


Literature

The structure of the harmonin/sans complex reveals an unexpected interaction mode of the two Usher syndrome proteins

Yan, J.Pan, L.Chen, X.Wu, L.Zhang, M.

(2010) Proc Natl Acad Sci U S A 107: 4040-4045

  • DOI: https://doi.org/10.1073/pnas.0911385107
  • Primary Citation of Related Structures:  
    3K1R

  • PubMed Abstract: 

    The hereditary hearing-vision loss disease, Usher syndrome I (USH1), is caused by defects in several proteins that can interact with each other in vitro. Defects in USH1 proteins are thought to be responsible for the developmental and functional impairments of sensory cells in the retina and inner ear. Harmonin/USH1C and Sans/USH1G are two of the USH1 proteins that interact with each other. Harmonin also binds to other USH1 proteins such as cadherin 23 (CDH23) and protocadherin 15 (PCDH15). However, the molecular basis governing the harmonin and Sans interaction is largely unknown. Here, we report an unexpected assembly mode between harmonin and Sans. We demonstrate that the N-terminal domain and the first PDZ domain of harmonin are tethered by a small-domain C-terminal to PDZ1 to form a structural and functional supramodule responsible for binding to Sans. We discover that the SAM domain of Sans, specifically, binds to the PDZ domain of harmonin, revealing previously unknown interaction modes for both PDZ and SAM domains. We further show that the synergistic PDZ1/SAM and PDZ1/carboxyl PDZ binding-motif interactions, between harmonin and Sans, lock the two scaffold proteins into a highly stable complex. Mutations in harmonin and Sans found in USH1 patients are shown to destabilize the complex formation of the two proteins.


  • Organizational Affiliation

    Department of Biochemistry, Molecular Neuroscience Center, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Harmonin192Homo sapiensMutation(s): 1 
Gene Names: USH1C
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6N9 (Homo sapiens)
Explore Q9Y6N9 
Go to UniProtKB:  Q9Y6N9
PHAROS:  Q9Y6N9
GTEx:  ENSG00000006611 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6N9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Usher syndrome type-1G protein74Homo sapiensMutation(s): 1 
Gene Names: USH1G
UniProt & NIH Common Fund Data Resources
Find proteins for Q495M9 (Homo sapiens)
Explore Q495M9 
Go to UniProtKB:  Q495M9
PHAROS:  Q495M9
GTEx:  ENSG00000182040 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ495M9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.603α = 90
b = 57.775β = 104.63
c = 59.505γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description