5K6Z

Sidekick chimera containing sidekick-2 immunoglobulin domains 1-2 and sidekick-1 immunoglobulin domains 3-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report



Literature

Molecular basis of sidekick-mediated cell-cell adhesion and specificity.

Goodman, K.M.Yamagata, M.Jin, X.Mannepalli, S.Katsamba, P.S.Ahlsen, G.Sergeeva, A.P.Honig, B.Sanes, J.R.Shapiro, L.

(2016) Elife 5

  • DOI: 10.7554/eLife.19058
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Sidekick (Sdk) 1 and 2 are related immunoglobulin superfamily cell adhesion proteins required for appropriate synaptic connections between specific subtypes of retinal neurons. Sdks mediate cell-cell adhesion with homophilic specificity that underlie ...

    Sidekick (Sdk) 1 and 2 are related immunoglobulin superfamily cell adhesion proteins required for appropriate synaptic connections between specific subtypes of retinal neurons. Sdks mediate cell-cell adhesion with homophilic specificity that underlies their neuronal targeting function. Here we report crystal structures of Sdk1 and Sdk2 ectodomain regions, revealing similar homodimers mediated by the four N-terminal immunoglobulin domains (Ig1-4), arranged in a horseshoe conformation. These Ig1-4 horseshoes interact in a novel back-to-back orientation in both homodimers through Ig1:Ig2, Ig1:Ig1 and Ig3:Ig4 interactions. Structure-guided mutagenesis results show that this canonical dimer is required for both Sdk-mediated cell aggregation (via trans interactions) and Sdk clustering in isolated cells (via cis interactions). Sdk1/Sdk2 recognition specificity is encoded across Ig1-4, with Ig1-2 conferring the majority of binding affinity and differential specificity. We suggest that competition between cis and trans interactions provides a novel mechanism to sharpen the specificity of cell-cell interactions.


    Organizational Affiliation

    Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein sidekick-2,Protein sidekick-1 chimera
A, B
384Mus musculusMutation(s): 0 
Gene Names: Sdk2Kiaa1514
Find proteins for Q6V4S5 (Mus musculus)
Go to UniProtKB:  Q6V4S5
Find proteins for Q3UH53 (Mus musculus)
Go to UniProtKB:  Q3UH53
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CAC
Query on CAC

Download CCD File 
B
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
MPD
Query on MPD

Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 2 21 21
  • Diffraction Data DOI: 10.15785/SBGRID/372 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.35α = 90
b = 85.73β = 90
c = 146.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release