Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 43.82 kDa 
• Atom Count: 3915 
• Modelled Residue Count: 388 
• Deposited Residue Count: 388 
• Unique protein chains: 1

2V5M

Structural basis for Dscam isoform specificity

• PDB DOI: 10.2210/pdb2V5M/pdb

• Classification: CELL ADHESION
• Organism(s): Drosophila melanogaster
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2007-07-06 Released: 2007-09-11 
• Deposition Author(s): Meijers, R., Puettmann-Holgado, R., Skiniotis, G., Liu, J.-H., Walz, T., Schmucker, D., Wang, J.-H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.205 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4XHQ

Literature

Structural Basis of Dscam Isoform Specificity

Meijers, R., Puettmann-Holgado, R., Skiniotis, G., Liu, J.-H., Walz, T., Wang, J.-H., Schmucker, D.

(2007) Nature 449: 487

• PubMed: 17721508 
• DOI: 10.1038/nature06147
• Primary Citation of Related Structures:  
  2V5M, 2V5R, 2V5S


• PubMed Abstract: 
  

The Dscam gene gives rise to thousands of diverse cell surface receptors thought to provide homophilic and heterophilic recognition specificity for neuronal wiring and immune responses. Mutually exclusive splicing allows for the generation of sequence variability in three immunoglobulin ecto-domains, D2, D3 and D7. We report X-ray structures of the amino-terminal four immunoglobulin domains (D1-D4) of two distinct Dscam isoforms. The structures reveal a horseshoe configuration, with variable residues of D2 and D3 constituting two independent surface epitopes on either side of the receptor. Both isoforms engage in homo-dimerization coupling variable domain D2 with D2, and D3 with D3. These interactions involve symmetric, antiparallel pairing of identical peptide segments from epitope I that are unique to each isoform. Structure-guided mutagenesis and swapping of peptide segments confirm that epitope I, but not epitope II, confers homophilic binding specificity of full-length Dscam receptors. Phylogenetic analysis shows strong selection of matching peptide sequences only for epitope I. We propose that peptide complementarity of variable residues in epitope I of Dscam is essential for homophilic binding specificity.

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Organizational Affiliation: 

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DSCAM	A	388	Drosophila melanogaster	Mutation(s): 20  Gene Names: Dscam1, Dscam, CG17800
UniProt
Find proteins for Q9NBA1 (Drosophila melanogaster) Explore Q9NBA1  Go to UniProtKB:  Q9NBA1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.205 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.172	α = 90
b = 99.172	β = 90
c = 163.991	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
SHARP	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-07-06 
• Released Date: 2007-09-11 
Deposition Author(s): Meijers, R., Puettmann-Holgado, R., Skiniotis, G., Liu, J.-H., Walz, T., Schmucker, D., Wang, J.-H.

Revision History  

• Version 1.0: 2007-09-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-10-23
  Changes: Data collection, Database references, Derived calculations, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary