6JMV

Crystal structure of the GluK3 ligand binding domain complex with SYM and zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural and Functional Insights into GluK3-kainate Receptor Desensitization and Recovery.

Kumari, J.Vinnakota, R.Kumar, J.

(2019) Sci Rep 9: 10254-10254

  • DOI: 10.1038/s41598-019-46770-z
  • Primary Citation of Related Structures:  
    6JFY, 6JFZ, 6JMV

  • PubMed Abstract: 
  • GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play a vital role in the regulation of synaptic transmission. For a better understanding of structural changes that underlie receptor functions, GluK3 receptors were trapped in desensitized and resting/closed states and structures analyzed using single particle cryo-electron microscopy ...

    GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play a vital role in the regulation of synaptic transmission. For a better understanding of structural changes that underlie receptor functions, GluK3 receptors were trapped in desensitized and resting/closed states and structures analyzed using single particle cryo-electron microscopy. While the desensitized GluK3 has domain organization as seen earlier for another kainate receptor-GluK2, antagonist bound GluK3 trapped a resting state with only two LBD domains in dimeric arrangement necessary for receptor activation. Using structures as a guide, we show that the N-linked glycans at the interface of GluK3 ATD and LBD likely mediate inter-domain interactions and attune receptor-gating properties. The mutational analysis also identified putative N-glycan interacting residues. Our results provide a molecular framework for understanding gating properties unique to GluK3 and exploring the role of N-linked glycosylation in their modulation.


    Organizational Affiliation

    Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Maharashtra, Pune, 411007, India. janesh@nccs.res.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, kainate 3A, B257Rattus norvegicusMutation(s): 0 
Gene Names: Grik3Glur7
Membrane Entity: Yes 
UniProt
Find proteins for P42264 (Rattus norvegicus)
Explore P42264 
Go to UniProtKB:  P42264
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42264
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SYM
Query on SYM

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
2S,4R-4-METHYLGLUTAMATE
C6 H10 N O4
KRKRAOXTGDJWNI-DMTCNVIQSA-M
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth A],
K [auth B],
M [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth A],
T [auth B],
U [auth B],
G [auth A],
H [auth A],
J [auth A],
T [auth B],
U [auth B],
V [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
N [auth B],
O [auth B],
W [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
X [auth B],
Y [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 2 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.46α = 90
b = 88.03β = 90
c = 130.47γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustIndiaIA/I/13/2/501023

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references