1MI1

Crystal Structure of the PH-BEACH Domain of Human Neurobeachin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1093/emboj/cdf502
  • Primary Citation of Related Structures:  
    1MI1

  • 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. ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NeurobeachinAB414Homo sapiensMutation(s): 0 
Gene Names: NBEABCL8BKIAA1544LYST2
Find proteins for Q8NFP9 (Homo sapiens)
Explore Q8NFP9 
Go to UniProtKB:  Q8NFP9
NIH Common Fund Data Resources
PHAROS  Q8NFP9
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
MADSYSphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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