4X83

Crystal structure of Dscam1 isoform 7.44, N-terminal four Ig domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.902 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of Dscam1 homodimerization: Insights into context constraint for protein recognition

Li, S.A.Cheng, L.Yu, Y.Chen, Q.

(2016) Sci Adv 2: e1501118-e1501118

  • DOI: 10.1126/sciadv.1501118
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Drosophila neural receptor Dscam1 (Down syndrome cell adhesion molecule 1) plays an essential role in neuronal wiring and self-avoidance. Dscam1 potentially encodes 19,008 ectodomains through alternative RNA splicing and exhibits exquisite isofor ...

    The Drosophila neural receptor Dscam1 (Down syndrome cell adhesion molecule 1) plays an essential role in neuronal wiring and self-avoidance. Dscam1 potentially encodes 19,008 ectodomains through alternative RNA splicing and exhibits exquisite isoform-specific homophilic binding, which makes it an exceptional example for studying protein binding specificity. However, structural information on Dscam1 is limited, which hinders illumination of the mechanism of Dscam1 isoform-specific recognition. Whether different Dscam1 isoforms adopt the same dimerization mode remains a subject of debate. We present 12 Dscam1 crystal structures, provide direct evidence indicating that all isoforms adopt a conserved homodimer geometry in a modular fashion, identify two mechanisms for the Ig2 binding domain to dispel electrostatic repulsion during dimerization, decode Ig2 binding specificity by a central motif at its symmetry center, uncover the role of glycosylation in Dscam1 homodimerization, and find electrostatic potential complementarity to help define the binding region and the antiparallel binding mode. We then propose a concept that the context of a protein may set restrictions to regulate its binding specificity, which provides a better understanding of protein recognition.


    Organizational Affiliation

    State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, P. R. China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Down syndrome cell adhesion molecule, isoform 7.44
A, B, C, D
394Drosophila melanogasterMutation(s): 0 
Gene Names: Dscam1 (43Bc, CT39257, Dm_2R:13579, Dm_2R:13612, DmDscam, Dmel\CG17800, DSCAM, DScam, DsCam, Dscam, dScam, dscam, Dscam-hv, dscam1, Dsm, FBgn0033159, l(2)05518, l(2)43Bc, Neu1, p270)
Find proteins for Q0E9K9 (Drosophila melanogaster)
Go to UniProtKB:  Q0E9K9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.902 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.734α = 98.18
b = 88.248β = 98.79
c = 94.310γ = 90.11
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references