7Y8S | pdb_00007y8s

Crystal structure of sDscam FNIII1-3 domains, isoform beta2v6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.275 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Y8S

This is version 1.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 66.11 kDa 
  • Atom Count: 4,508 
  • Modeled Residue Count: 563 
  • Deposited Residue Count: 596 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dscam
A, B
298ChelicerataMutation(s): 0 
Gene Names: Dscam
UniProt
Find proteins for A0A161FW14 (Olivierus martensii)
Explore A0A161FW14 
Go to UniProtKB:  A0A161FW14
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A161FW14
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.275 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.649α = 90
b = 171.649β = 90
c = 114.933γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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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