4YKI

Mnemiopsis leidyi ML032222a iGluR LBD glycine complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Glycine activated ion channel subunits encoded by ctenophore glutamate receptor genes.

Alberstein, R.Grey, R.Zimmet, A.Simmons, D.K.Mayer, M.L.

(2015) Proc.Natl.Acad.Sci.USA 112: E6048-E6057

  • DOI: 10.1073/pnas.1513771112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recent genome projects for ctenophores have revealed the presence of numerous ionotropic glutamate receptors (iGluRs) in Mnemiopsis leidyi and Pleurobrachia bachei, among our earliest metazoan ancestors. Sequence alignments and phylogenetic analysis ...

    Recent genome projects for ctenophores have revealed the presence of numerous ionotropic glutamate receptors (iGluRs) in Mnemiopsis leidyi and Pleurobrachia bachei, among our earliest metazoan ancestors. Sequence alignments and phylogenetic analysis show that these form a distinct clade from the well-characterized AMPA, kainate, and NMDA iGluR subtypes found in vertebrates. Although annotated as glutamate and kainate receptors, crystal structures of the ML032222a and PbiGluR3 ligand-binding domains (LBDs) reveal endogenous glycine in the binding pocket, whereas ligand-binding assays show that glycine binds with nanomolar affinity; biochemical assays and structural analysis establish that glutamate is occluded from the binding cavity. Further analysis reveals ctenophore-specific features, such as an interdomain Arg-Glu salt bridge, present only in subunits that bind glycine, but also a conserved disulfide in loop 1 of the LBD that is found in all vertebrate NMDA but not AMPA or kainate receptors. We hypothesize that ctenophore iGluRs are related to an early ancestor of NMDA receptors, suggesting a common evolutionary path for ctenophores and bilaterian species, and suggest that future work should consider both glycine and glutamate as candidate neurotransmitters in ctenophore species.


    Organizational Affiliation

    Laboratory of Cellular and Molecular Neurophysiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ML032222a iGluR
A, B
256Mnemiopsis leidyiMutation(s): 0 
Find proteins for A0A0R4I973 (Mnemiopsis leidyi)
Go to UniProtKB:  A0A0R4I973
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

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A, B
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.134 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.944α = 90.00
b = 123.388β = 111.84
c = 54.319γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references
  • Version 1.2: 2015-11-18
    Type: Database references