6KYH

Crystal structure of Shank3 NTD-ANK A42K mutant in complex with HRas


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Shank3 Binds to and Stabilizes the Active Form of Rap1 and HRas GTPases via Its NTD-ANK Tandem with Distinct Mechanisms.

Cai, Q.Hosokawa, T.Zeng, M.Hayashi, Y.Zhang, M.

(2020) Structure 28: 290

  • DOI: https://doi.org/10.1016/j.str.2019.11.018
  • Primary Citation of Related Structures:  
    6KYH, 6KYK

  • PubMed Abstract: 

    Shank1/2/3, major scaffold proteins in excitatory synapses, are frequently mutated in patients with psychiatric disorders. Although the Shank N-terminal domain and ankyrin repeats domain tandem (NTD-ANK) is known to bind to Ras and Rap1, the molecular mechanism underlying and functional significance of the bindings in synapses are unknown. Here, we demonstrate that Shank3 NTD-ANK specifically binds to the guanosine triphosphate (GTP)-bound form of HRas and Rap1. In addition to the canonical site mediated by the Ras-association domain and common to both GTPases, Shank3 contains an unconventional Rap1 binding site formed by NTD and ANK together. Binding of Shank3 to the GTP-loaded Rap1 slows down its GTP hydrolysis by SynGAP. We further show that the interactions between Shank3 and HRas/Rap1 at excitatory synapses are promoted by synaptic activation. Thus, Shank3 may be able to modulate signaling of the Ras family proteins via directly binding to and stabilizing the GTP-bound form of the enzymes.


  • 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
SH3 and multiple ankyrin repeat domains protein 3
A, B, C, D
361Mus musculusMutation(s): 3 
Gene Names: Shank3Kiaa1650Prosap2
UniProt & NIH Common Fund Data Resources
Find proteins for Q4ACU6 (Mus musculus)
Explore Q4ACU6 
Go to UniProtKB:  Q4ACU6
IMPC:  MGI:1930016
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4ACU6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase HRasE [auth F],
F [auth G],
G [auth H],
H [auth E]
171Mus musculusMutation(s): 0 
Gene Names: HrasHras1
UniProt
Find proteins for Q61411 (Mus musculus)
Explore Q61411 
Go to UniProtKB:  Q61411
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ61411
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.569α = 90
b = 154.464β = 108.35
c = 116.949γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong KongAoE-M09-12

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Database references
  • Version 1.2: 2020-03-18
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description