Crystal Structure of the PH-BEACH Domain of Human Neurobeachin

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

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Crystal structure of the BEACH domain reveals an unusual fold and extensive association with a novel PH domain.

Jogl, G.Shen, Y.Gebauer, D.Li, J.Wiegmann, K.Kashkar, H.Kronke, M.Tong, L.

(2002) EMBO J 21: 4785-4795

  • DOI: https://doi.org/10.1093/emboj/cdf502
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The BEACH domain is highly conserved in a large family of eukaryotic proteins, and is crucial for their functions in vesicle trafficking, membrane dynamics and receptor signaling. However, it does not share any sequence homology with other proteins. Here we report the crystal structure at 2.9 A resolution of the BEACH domain of human neurobeachin. It shows that the BEACH domain has a new and unusual polypeptide backbone fold, as the peptide segments in its core do not assume regular secondary structures. Unexpectedly, the structure also reveals that the BEACH domain is in extensive association with a novel, weakly conserved pleckstrin-homology (PH) domain. Consistent with the structural analysis, biochemical studies show that the PH and BEACH domains have strong interactions, suggesting they may function as a single unit. Functional studies in intact cells demonstrate the requirement of both the PH and the BEACH domains for activity. A prominent groove at the interface between the two domains may be used to recruit their binding partners.

  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
414Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFP9 (Homo sapiens)
Explore Q8NFP9 
Go to UniProtKB:  Q8NFP9
GTEx:  ENSG00000172915 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NFP9
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.91α = 90
b = 179.91β = 90
c = 98.54γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance