7LZH

Structure of the glutamate receptor-like channel AtGLR3.4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the Arabidopsis thaliana glutamate receptor-like channel GLR3.4.

Green, M.N.Gangwar, S.P.Michard, E.Simon, A.A.Portes, M.T.Barbosa-Caro, J.Wudick, M.M.Lizzio, M.A.Klykov, O.Yelshanskaya, M.V.Feijo, J.A.Sobolevsky, A.I.

(2021) Mol Cell 81: 3216

  • DOI: https://doi.org/10.1016/j.molcel.2021.05.025
  • Primary Citation of Related Structures:  
    7LZ0, 7LZ1, 7LZ2, 7LZH, 7LZI

  • PubMed Abstract: 

    Glutamate receptor-like channels (GLRs) play vital roles in various physiological processes in plants, such as wound response, stomatal aperture control, seed germination, root development, innate immune response, pollen tube growth, and morphogenesis. Despite the importance of GLRs, knowledge about their molecular organization is limited. Here we use X-ray crystallography and single-particle cryo-EM to solve structures of the Arabidopsis thaliana GLR3.4. Our structures reveal the tetrameric assembly of GLR3.4 subunits into a three-layer domain architecture, reminiscent of animal ionotropic glutamate receptors (iGluRs). However, the non-swapped arrangement between layers of GLR3.4 domains, binding of glutathione through S-glutathionylation of cysteine C205 inside the amino-terminal domain clamshell, unique symmetry, inter-domain interfaces, and ligand specificity distinguish GLR3.4 from representatives of the iGluR family and suggest distinct features of the GLR gating mechanism. Our work elaborates on the principles of GLR architecture and symmetry and provides a molecular template for deciphering GLR-dependent signaling mechanisms in plants.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA; Training Program in Nutritional and Metabolic Biology, Institute of Human Nutrition, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 3.4
A, B, C, D
959Arabidopsis thalianaMutation(s): 0 
Gene Names: GLR3.4GLR4GLUR3At1g05200YUP8H12.19
Membrane Entity: Yes 
UniProt
Find proteins for Q8GXJ4 (Arabidopsis thaliana)
Explore Q8GXJ4 
Go to UniProtKB:  Q8GXJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GXJ4
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H, I
E, F, G, H, I, J, K, L
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSH (Subject of Investigation/LOI)
Query on GSH

Download Ideal Coordinates CCD File 
BA [auth D],
P [auth A],
T [auth B],
X [auth C]
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth D]
N [auth A]
O [auth A]
R [auth B]
S [auth B]
AA [auth D],
N [auth A],
O [auth A],
R [auth B],
S [auth B],
V [auth C],
W [auth C],
Z [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLU (Subject of Investigation/LOI)
Query on GLU

Download Ideal Coordinates CCD File 
M [auth A],
Q [auth B],
U [auth C],
Y [auth D]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA206573
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS083660
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS107253
National Science Foundation (NSF, United States)United States1818086

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references