2UXA | pdb_00002uxa

Crystal structure of the GluR2-flip ligand binding domain, r/g unedited.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 
    0.265 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2UXA

This is version 1.4 of the entry. See complete history

Literature

Developmentally Regulated, Combinatorial RNA Processing Modulates Ampa Receptor Biogenesis.

Greger, I.H.Akamine, P.Khatri, L.Ziff, E.B.

(2006) Neuron 51: 85

  • DOI: https://doi.org/10.1016/j.neuron.2006.05.020

  • PubMed Abstract: 

    The subunit composition determines AMPA receptor (AMPA-R) function and trafficking. Mechanisms underlying channel assembly are thus central to the efficacy and plasticity of glutamatergic synapses. We previously showed that RNA editing at the Q/R site of the GluR2 subunit contributes to the assembly of AMPA-R heteromers by attenuating formation of GluR2 homotetramers. Here we report that this function of the Q/R site depends on subunit contacts between adjacent ligand binding domains (LBDs). Changes of LBD interface contacts alter GluR2 assembly properties, forward traffic, and expression at synapses. Interestingly, developmentally regulated RNA editing within the LBD (at the R/G site) produces analogous effects. Our data reveal that editing to glycine reduces the self-assembly competence of this critical subunit and slows GluR2 maturation in the endoplasmic reticulum (ER). Therefore, RNA editing sites, located at strategic subunit interfaces, shape AMPA-R assembly and trafficking in a developmentally regulated manner.


  • Organizational Affiliation
    • Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom. ig@mrc-lmb.cam.ac.uk

Macromolecule Content 

  • Total Structure Weight: 88.39 kDa 
  • Atom Count: 6,535 
  • Modeled Residue Count: 781 
  • Deposited Residue Count: 783 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLUTAMATE RECEPTOR SUBUNIT GLUR2-FLIP
A, B, C
261Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19491
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLU

Query on GLU



Download:Ideal Coordinates CCD File
D [auth A],
F [auth B],
I [auth C]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
H [auth B],
J [auth C],
K [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free:  0.265 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.254α = 90
b = 164.003β = 90
c = 47.462γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2011-06-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary