7Y6O | pdb_00007y6o

Crystal structure of sDscam Ig1-3 domains, isoform alpha25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.287 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.251 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.253 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis for the self-recognition of sDSCAM in Chelicerata.

Cheng, J.Yu, Y.Wang, X.Zheng, X.Liu, T.Hu, D.Jin, Y.Lai, Y.Fu, T.M.Chen, Q.

(2023) Nat Commun 14: 2522-2522

  • DOI: https://doi.org/10.1038/s41467-023-38205-1
  • Primary Citation of Related Structures:  
    7Y4X, 7Y54, 7Y5J, 7Y5R, 7Y6E, 7Y6O, 7Y73, 7Y8H, 7Y8I, 7Y8S, 7Y95, 7Y9A

  • PubMed Abstract: 

    To create a functional neural circuit, neurons develop a molecular identity to discriminate self from non-self. The invertebrate Dscam family and vertebrate Pcdh family are implicated in determining synaptic specificity. Recently identified in Chelicerata, a shortened Dscam (sDscam) has been shown to resemble the isoform-generating characters of both Dscam and Pcdh and represent an evolutionary transition. Here we presented the molecular details of sDscam self-recognition via both trans and cis interactions using X-ray crystallographic data and functional assays. Based on our results, we proposed a molecular zipper model for the assemblies of sDscam to mediate cell-cell recognition. In this model, sDscam utilized FNIII domain to form side-by-side interactions with neighboring molecules in the same cell while established hand-in-hand interactions via Ig1 domain with molecules from another cell around. Together, our study provided a framework for understanding the assembly, recognition, and evolution of sDscam.


  • Organizational Affiliation
    • National Clinical Research Center for Geriatrics, West China Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, 610041, Chengdu, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Down Syndrome Cell Adhesion Molecules295ChelicerataMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.287 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.251 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.253 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.484α = 90
b = 117.484β = 90
c = 171.494γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary