7Y95 | pdb_00007y95

Crystal structure of sDscam Ig1 domain, isoform beta6v2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.191 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.152 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Y95

Ligand Structure Quality Assessment 


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 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: 21.77 kDa 
  • Atom Count: 1,762 
  • Modeled Residue Count: 198 
  • Deposited Residue Count: 200 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dscam
A, B
100ChelicerataMutation(s): 0 
Gene Names: Dscam
UniProt
Find proteins for A0A159W5Q3 (Olivierus martensii)
Explore A0A159W5Q3 
Go to UniProtKB:  A0A159W5Q3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A159W5Q3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
(Subject of Investigation/LOI)

Query on GOL



Download:Ideal Coordinates CCD File
I [auth B],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
(Subject of Investigation/LOI)

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.191 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.177α = 90
b = 39.096β = 108.97
c = 60.873γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



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: 2024-11-13
    Changes: Structure summary