3COO

The crystal structure of Reelin-N domain of F-spondin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of the heparin-binding reelin-N domain of f-spondin.

Tan, K.Duquette, M.Liu, J.H.Lawler, J.Wang, J.H.

(2008) J.Mol.Biol. 381: 1213-1223

  • DOI: 10.1016/j.jmb.2008.06.045

  • PubMed Abstract: 
  • The extracellular matrix protein F-spondin mediates axon guidance during neuronal development. Its N-terminal domain, termed the reelin-N domain, is conserved in F-spondins, reelins, and other extracellular matrix proteins. In this study, a recombina ...

    The extracellular matrix protein F-spondin mediates axon guidance during neuronal development. Its N-terminal domain, termed the reelin-N domain, is conserved in F-spondins, reelins, and other extracellular matrix proteins. In this study, a recombinant human reelin-N domain has been expressed, purified, and shown to bind heparin. The crystal structure of the reelin-N domain resolved to 2.0 A reveals a variant immunoglobulin-like fold and potential heparin-binding sites. Substantial conformational variations even in secondary structure are observed between the two chemically identical reelin-N domains in one crystallographic asymmetric unit. The variations may result from extensive, highly specific interactions across the interface of the two reelin-N domains. The calculated values of buried surface area and the interface's shape complementarity are consistent with the formation of a weak dimer. The homophilic asymmetric dimer can potentially offer advantages in binding to ligands such as glycosaminoglycans, which may, in turn, bridge the two reelin-N domains and stabilize the dimer.


    Organizational Affiliation

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. ktan@anl.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spondin-1
A, B
180Homo sapiensMutation(s): 0 
Gene Names: SPON1 (KIAA0762, VSGP)
Find proteins for Q9HCB6 (Homo sapiens)
Go to Gene View: SPON1
Go to UniProtKB:  Q9HCB6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.605α = 90.00
b = 58.605β = 90.00
c = 219.542γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
RESOLVEphasing
HKL-2000data reduction
SHELXDphasing
DMphasing
SBC-Collectdata collection
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description