5L5N

Plexin A4 full extracellular region, domains 1 to 7 modeled, data to 8.5 angstrom, spacegroup P4(3)22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.50 Å
  • R-Value Free: 0.412 
  • R-Value Work: 0.401 
  • R-Value Observed: 0.402 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural Basis for Plexin Activation and Regulation.

Kong, Y.Janssen, B.J.Malinauskas, T.Vangoor, V.R.Coles, C.H.Kaufmann, R.Ni, T.Gilbert, R.J.Padilla-Parra, S.Pasterkamp, R.J.Jones, E.Y.

(2016) Neuron 91: 548-560

  • DOI: https://doi.org/10.1016/j.neuron.2016.06.018
  • Primary Citation of Related Structures:  
    5L56, 5L59, 5L5C, 5L5G, 5L5K, 5L5L, 5L5M, 5L5N, 5L74, 5L7N

  • PubMed Abstract: 

    Class A plexins (PlxnAs) act as semaphorin receptors and control diverse aspects of nervous system development and plasticity, ranging from axon guidance and neuron migration to synaptic organization. PlxnA signaling requires cytoplasmic domain dimerization, but extracellular regulation and activation mechanisms remain unclear. Here we present crystal structures of PlxnA (PlxnA1, PlxnA2, and PlxnA4) full ectodomains. Domains 1-9 form a ring-like conformation from which the C-terminal domain 10 points away. All our PlxnA ectodomain structures show autoinhibitory, intermolecular "head-to-stalk" (domain 1 to domain 4-5) interactions, which are confirmed by biophysical assays, live cell fluorescence microscopy, and cell-based and neuronal growth cone collapse assays. This work reveals a 2-fold role of the PlxnA ectodomains: imposing a pre-signaling autoinhibitory separation for the cytoplasmic domains via intermolecular head-to-stalk interactions and supporting dimerization-based PlxnA activation upon ligand binding. More generally, our data identify a novel molecular mechanism for preventing premature activation of axon guidance receptors.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Plexin-A41,207Mus musculusMutation(s): 0 
Gene Names: Plxna4Kiaa1550
UniProt & NIH Common Fund Data Resources
Find proteins for Q80UG2 (Mus musculus)
Explore Q80UG2 
Go to UniProtKB:  Q80UG2
IMPC:  MGI:2179061
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80UG2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.50 Å
  • R-Value Free: 0.412 
  • R-Value Work: 0.401 
  • R-Value Observed: 0.402 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.48α = 90
b = 189.48β = 90
c = 252.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references
  • Version 1.2: 2016-08-17
    Changes: Database references
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary