7Y8I

Crystal structure of sDscam FNIII3 domain, isoform alpha7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


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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
Dscam
A, B, C, D, E
A, B, C, D, E, F
97ChelicerataMutation(s): 0 
Gene Names: Dscam
UniProt
Find proteins for A0A159W468 (Mesobuthus martensii)
Explore A0A159W468 
Go to UniProtKB:  A0A159W468
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A159W468
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG (Subject of Investigation/LOI)
Query on PEG

Download Ideal Coordinates CCD File 
P [auth F]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
J [auth B]
L [auth D]
M [auth E]
G [auth A],
I [auth B],
J [auth B],
L [auth D],
M [auth E],
N [auth E],
Q [auth F],
R [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
IPA (Subject of Investigation/LOI)
Query on IPA

Download Ideal Coordinates CCD File 
H [auth B],
K [auth C]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
O [auth E]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.113α = 90
b = 85.776β = 90
c = 106.238γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
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