5L5C

Plexin A1 full extracellular region, domains 1 to 10, to 6 angstrom, spacegroup P4(3)2(1)2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.305 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1016/j.neuron.2016.06.018
  • Primary Citation of Related Structures:  

  • 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 dimer ...

    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.,Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Department of Biochemistry, University of Oxford, Oxford, United Kingdom.,Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands. Electronic address: r.j.pasterkamp@umcutrecht.nl.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom. Electronic address: yvonne@strubi.ox.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plexin-A1
A
1212Mus musculusMutation(s): 0 
Gene Names: Plxna1 (Kiaa4053)
Find proteins for P70206 (Mus musculus)
Go to UniProtKB:  P70206
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.305 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 198.150α = 90.00
b = 198.150β = 90.00
c = 228.900γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALAdata scaling
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-20
    Type: Database references
  • Version 1.2: 2016-08-17
    Type: Database references
  • Version 1.3: 2018-05-23
    Type: Advisory, Data collection, Derived calculations
  • Version 1.4: 2018-10-24
    Type: Advisory, Data collection, Derived calculations