3DMK

Crystal structure of Down Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.19 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.282 

wwPDB Validation 3D Report Full Report



Literature

A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms.

Sawaya, M.R.Wojtowicz, W.M.Andre, I.Qian, B.Wu, W.Baker, D.Eisenberg, D.Zipursky, S.L.

(2008) Cell 134: 1007-1018

  • DOI: 10.1016/j.cell.2008.07.042
  • Primary Citation of Related Structures:  
    3DMK

  • PubMed Abstract: 
  • Drosophila Dscam encodes a vast family of immunoglobulin (Ig)-containing proteins that exhibit isoform-specific homophilic binding. This diversity is essential for cell recognition events required for wiring the brain. Each isoform binds to itself bu ...

    Drosophila Dscam encodes a vast family of immunoglobulin (Ig)-containing proteins that exhibit isoform-specific homophilic binding. This diversity is essential for cell recognition events required for wiring the brain. Each isoform binds to itself but rarely to other isoforms. Specificity is determined by "matching" of three variable Ig domains within an approximately 220 kD ectodomain. Here, we present the structure of the homophilic binding region of Dscam, comprising the eight N-terminal Ig domains (Dscam(1-8)). Dscam(1-8) forms a symmetric homodimer of S-shaped molecules. This conformation, comprising two reverse turns, allows each pair of the three variable domains to "match" in an antiparallel fashion. Structural, genetic, and biochemical studies demonstrate that, in addition to variable domain "matching," intramolecular interactions between constant domains promote homophilic binding. These studies provide insight into how "matching" at all three pairs of variable domains in Dscam mediates isoform-specific recognition.


    Organizational Affiliation

    Howard Hughes Medical Institute, UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, CA 90095, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Down Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domainsABC816Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for Q0E9I4 (Drosophila melanogaster)
Explore Q0E9I4 
Go to UniProtKB:  Q0E9I4
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F, I
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, J, K
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900017
Query on PRD_900017
G, H, J, Ktriacetyl-beta-chitotrioseOligosaccharide /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.19 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.282 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.46α = 90
b = 177.61β = 90
c = 434.05γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary