6NRQ

Crystal structure of Dpr10 IG1 bound to DIP-alpha IG1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report

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This is version 2.1 of the entry. See complete history


Literature

Molecular basis of synaptic specificity by immunoglobulin superfamily receptors in Drosophila.

Cheng, S.Ashley, J.Kurleto, J.D.Lobb-Rabe, M.Park, Y.J.Carrillo, R.A.Ozkan, E.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.41028
  • Primary Citation of Related Structures:  
    6NRQ, 6NRR, 6NRW, 6NRX, 6NS1

  • PubMed Abstract: 

    In stereotyped neuronal networks, synaptic connectivity is dictated by cell surface proteins, which assign unique identities to neurons, and physically mediate axon guidance and synapse targeting. We recently identified two groups of immunoglobulin superfamily proteins in Drosophila , Dprs and DIPs, as strong candidates for synapse targeting functions. Here, we uncover the molecular basis of specificity in Dpr-DIP mediated cellular adhesions and neuronal connectivity. First, we present five crystal structures of Dpr-DIP and DIP-DIP complexes, highlighting the evolutionary and structural origins of diversification in Dpr and DIP proteins and their interactions. We further show that structures can be used to rationally engineer receptors with novel specificities or modified affinities, which can be used to study specific circuits that require Dpr-DIP interactions to help establish connectivity. We investigate one pair, engineered Dpr10 and DIP-α, for function in the neuromuscular circuit in flies, and reveal roles for homophilic and heterophilic binding in wiring.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Defective proboscis extension response 10, isoform A
A, C
113Drosophila melanogasterMutation(s): 0 
Gene Names: dpr10BcDNA:RE37920CG14158CG14159CT33762Dmel\CG32057Dpr-10Dpr10CG32057Dmel_CG32057
UniProt
Find proteins for Q9VT83 (Drosophila melanogaster)
Explore Q9VT83 
Go to UniProtKB:  Q9VT83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VT83
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dpr-interacting protein alpha, isoform A
B, D
113Drosophila melanogasterMutation(s): 0 
Gene Names: DIP-alpha32791CG13019CG13020Dmel\CG32791CG32791Dmel_CG32791
UniProt
Find proteins for Q9W4R3 (Drosophila melanogaster)
Explore Q9W4R3 
Go to UniProtKB:  Q9W4R3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9W4R3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
E, H
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G63564LA
GlyCosmos:  G63564LA
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
F, G
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G17601US
GlyCosmos:  G17601US
GlyGen:  G17601US
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.011α = 119.68
b = 53.551β = 103.77
c = 56.685γ = 92.88
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS097161

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary