5ZZ9

Crystal structure of Homer2 EVH1/Drebrin PPXXF complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Homer Tetramer Promotes Actin Bundling Activity of Drebrin.

Li, Z.Liu, H.Li, J.Yang, Q.Feng, Z.Li, Y.Yang, H.Yu, C.Wan, J.Liu, W.Zhang, M.

(2019) Structure 27: 27-38.e4

  • DOI: https://doi.org/10.1016/j.str.2018.10.011
  • Primary Citation of Related Structures:  
    5ZZ9

  • PubMed Abstract: 

    Drebrin is an actin bundling protein that plays critical roles in synaptic spine development and plasticity. Homer, one of the most abundant scaffolding proteins in postsynaptic density, interacts with Drebrin's C-terminal PPXXF motifs using its Ena/VASP homology 1 (EVH1) domain. However, the molecular mechanism and biological function of this interaction remain unclear. Here we show that Homer specifically binds to the first but not the second PPXXF motif in Drebrin. The crystal structure of Drebrin-Homer binding motif 1 in complex with Homer EVH1 reveals a consensus Homer EVH1 binding motif. Homer tetramer promotes actin bundling activity of Drebrin in vitro and stimulates Drebrin-induced filopodia formation and elongation in cells. We further show that monomeric Homer1a antagonizes Homer1b in promoting Drebrin-stimulated actin bundling. Our study suggests a potential regulatory role of Homer1 in modulating excitatory synaptic spine homeostatic scaling via binding to Drebrin.


  • Organizational Affiliation

    Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homer protein homolog 2
A, B, C
123Mus musculusMutation(s): 0 
Gene Names: Homer2Vesl2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QWW1 (Mus musculus)
Explore Q9QWW1 
Go to UniProtKB:  Q9QWW1
IMPC:  MGI:1347354
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QWW1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Drebrin
D, E, F
28Homo sapiensMutation(s): 0 
Gene Names: DBN1D0S117E
UniProt & NIH Common Fund Data Resources
Find proteins for Q16643 (Homo sapiens)
Explore Q16643 
Go to UniProtKB:  Q16643
PHAROS:  Q16643
GTEx:  ENSG00000113758 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16643
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.337α = 70.44
b = 47.808β = 83.56
c = 50.415γ = 90.39
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Minister of Science and Technology of ChinaChina2014CB910204

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description