8B10

Crystal Structure of Shank2-SAM mutant domain - L1800W


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural deficits in key domains of Shank2 lead to alterations in postsynaptic nanoclusters and to a neurodevelopmental disorder in humans.

Hassani Nia, F.Woike, D.Bento, I.Niebling, S.Tibbe, D.Schulz, K.Hirnet, D.Skiba, M.Honck, H.H.Veith, K.Gunther, C.Scholz, T.Bierhals, T.Driemeyer, J.Bend, R.Failla, A.V.Lohr, C.Alai, M.G.Kreienkamp, H.J.

(2024) Mol Psychiatry 29: 1683-1697

  • DOI: https://doi.org/10.1038/s41380-022-01882-3
  • Primary Citation of Related Structures:  
    8ATJ, 8B10

  • PubMed Abstract: 

    Postsynaptic scaffold proteins such as Shank, PSD-95, Homer and SAPAP/GKAP family members establish the postsynaptic density of glutamatergic synapses through a dense network of molecular interactions. Mutations in SHANK genes are associated with neurodevelopmental disorders including autism and intellectual disability. However, no SHANK missense mutations have been described which interfere with the key functions of Shank proteins believed to be central for synapse formation, such as GKAP binding via the PDZ domain, or Zn 2+ -dependent multimerization of the SAM domain. We identify two individuals with a neurodevelopmental disorder carrying de novo missense mutations in SHANK2. The p.G643R variant distorts the binding pocket for GKAP in the Shank2 PDZ domain and prevents interaction with Thr(-2) in the canonical PDZ ligand motif of GKAP. The p.L1800W variant severely delays the kinetics of Zn 2+ -dependent polymerization of the Shank2-SAM domain. Structural analysis shows that Trp1800 dislodges one histidine crucial for Zn 2+ binding. The resulting conformational changes block the stacking of helical polymers of SAM domains into sheets through side-by-side contacts, which is a hallmark of Shank proteins, thereby disrupting the highly cooperative assembly process induced by Zn 2+ . Both variants reduce the postsynaptic targeting of Shank2 in primary cultured neurons and alter glutamatergic synaptic transmission. Super-resolution microscopy shows that both mutants interfere with the formation of postsynaptic nanoclusters. Our data indicate that both the PDZ- and the SAM-mediated interactions of Shank2 contribute to the compaction of postsynaptic protein complexes into nanoclusters, and that deficiencies in this process interfere with normal brain development in humans.


  • Organizational Affiliation

    Institute for Human Genetics, University Medical Center Hamburg Eppendorf, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SH3 and multiple ankyrin repeat domains protein 2
A, B, C, D, E
A, B, C, D, E, F
70Homo sapiensMutation(s): 1 
Gene Names: SHANK2CORTBP1KIAA1022PROSAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPX8 (Homo sapiens)
Explore Q9UPX8 
Go to UniProtKB:  Q9UPX8
PHAROS:  Q9UPX8
GTEx:  ENSG00000162105 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UPX8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.94α = 90
b = 135.282β = 90
c = 131.548γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyKr1321/9-1

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-09-11
    Changes: Database references